The cortex is the thick middle layer of a human hair strand, making up the vast majority of the fiber’s mass. Sandwiched between the thin outer cuticle (the shingle-like protective coating you can feel) and the sometimes-hollow medulla at the very center, the cortex is where most of hair’s defining properties originate. Your hair’s strength, elasticity, color, and curl pattern are all determined primarily by what is happening inside this layer, which is built from tightly packed, spindle-shaped cells filled with the protein keratin.
What the Cortex Looks Like Up Close
Under a microscope, the cortex appears as long, narrow cells stacked parallel to each other like bundles of logs running the length of the hair shaft. These cortical cells measure roughly 1 to 6 micrometers across and 50 to 100 micrometers long, so they are far longer than they are wide.1PeerJ. The structure of people’s hair Each cell is packed with even smaller substructures called macrofibrils, which are themselves bundles of microfibrils (also called intermediate filaments). These filaments are made of keratin proteins wound together in a helical arrangement, somewhat like the strands of a rope twisted around each other. Between and around these filaments sits a sulfur-rich matrix of smaller proteins called keratin-associated proteins (KAPs), which act as a kind of biological cement holding the filaments in place.
This layered, rope-within-a-rope architecture is what gives hair its remarkable combination of flexibility and strength. A single strand of hair can support a surprising amount of weight before snapping, and that tensile strength comes almost entirely from the cortex’s internal scaffolding.
Why the Cortex Controls Curl Pattern
Not all cortical cells are identical. Researchers have identified at least three subtypes within the cortex, called orthocortex, paracortex, and mesocortex. These differ in how their internal keratin filaments are packed and oriented. The distribution of these cell types around the cross-section of a hair strand turns out to be one of the main factors that determines whether your hair grows straight, wavy, or tightly coiled.
In straight hair, the orthocortex and paracortex tend to be distributed symmetrically around the fiber. In curly or coiled hair, these cell types are arranged asymmetrically, with one type concentrated on one side and the other on the opposite side.1PeerJ. The structure of people’s hair Because the two cell types swell and shrink slightly differently in response to moisture and have different internal structures, this lopsided arrangement causes the fiber to bend as it grows. Think of it like a bimetallic strip in a thermostat: two materials bonded together that expand at different rates will curve. The same basic principle applies inside a curly hair strand, with the orthocortex and paracortex playing the role of the two metals.
This means curl pattern is not just about the shape of the hair follicle (though that matters too). It is literally built into the internal arrangement of the cortex itself, cell by cell.
The Chemical Bonds That Give Hair Its Strength
Three main types of chemical bonds within the cortex are responsible for hair’s mechanical behavior: disulfide bonds, hydrogen bonds, and ionic (salt) bonds. Each plays a different role, and understanding the balance between them helps explain why hair behaves so differently when it is wet versus dry, or why chemical treatments can permanently alter its texture.
Disulfide bonds are the strongest of the three. They form between sulfur-containing amino acids (cysteine residues) in neighboring keratin chains, creating cross-links that lock the protein structure in place. These bonds are what give hair its permanent shape and are the reason hair holds its form even under stress. Breaking and reforming disulfide bonds is the mechanism behind permanent waves and chemical straightening treatments. Cysteine residues serve a dual role in the cortex: most of them stabilize the overall assembly of keratins and their associated proteins, but a proportion of the disulfide bonds between molecules are associated with the fiber’s mechanical flexibility.2PubMed Central. The susceptibility of disulfide bonds to modification in keratin fibers undergoing tensile stress
Hydrogen bonds are individually much weaker but exist in enormous numbers throughout the cortex. They are easily broken by water, which is why wet hair stretches more and behaves differently than dry hair. When you blow-dry or flat-iron your hair into a temporary new shape, you are breaking hydrogen bonds with heat and moisture and then letting them reform in a new configuration as the hair cools and dries. The effect lasts only until the hair gets wet again.
Ionic bonds form between positively and negatively charged amino acid side chains. They are sensitive to pH changes, which is why extremely alkaline or acidic solutions can weaken hair. The interplay among all three bond types, plus the contribution of hydrophobic interactions between non-polar regions of the proteins, collectively determines the fiber’s overall behavior and resilience.3PubMed. Chemical bonds and hair behaviour-A review
How the Cortex Handles Mechanical Stress
When you pull on a strand of hair, the cortex goes through a fascinating structural transformation. The keratin proteins in the cortex are normally arranged in a helical shape called an alpha-helix, a coiled spring-like configuration. Under tension, these helices begin to unwind and can transform into a flattened arrangement called a beta-sheet structure. This transition is what allows hair to stretch considerably, sometimes up to about 30 percent of its original length when dry, before breaking.4PubMed. Structure and mechanical behavior of human hair
This alpha-to-beta transition is reversible up to a point. If you stretch hair gently and release it, the helices spring back and the hair returns to its original length. Push past a certain threshold, though, and the transformation becomes permanent, meaning the internal protein structure of the cortex has been irreversibly altered. Wet hair reaches this point more easily because water disrupts many of the hydrogen bonds that normally reinforce the alpha-helical structure. When the disulfide bonds within the cortex were studied under wet and dry conditions, researchers found that different regions of the keratin molecules became vulnerable depending on whether hydrogen bonds were intact. In wet fibers, disulfide labeling appeared primarily in the head and tail domains of keratin chains, while in dry fibers, even the central rod domains showed susceptibility.2PubMed Central. The susceptibility of disulfide bonds to modification in keratin fibers undergoing tensile stress This helps explain why hair is more fragile when wet and more prone to breakage from rough handling, brushing, or tight styling.
Where Hair Color Comes From
Hair color is determined by pigment granules called melanosomes that sit within the cortex. These granules are produced by specialized cells (melanocytes) at the base of the hair follicle and are transferred into the cortical cells as they form. The type of melanin inside the granules, whether it is the darker eumelanin or the reddish-yellow pheomelanin, along with the size, shape, density, and distribution of the granules themselves, collectively produces the full spectrum of natural hair colors from jet black to platinum blonde to red.
Melanosomes are not static structures over a lifetime. Research comparing hair samples across age groups has found that the granules tend to enlarge with age. In the oldest individuals studied, the estimated volume of individual melanosomes was roughly twice that seen in children’s hair. This enlargement appears to be connected to the shift in hair color that many people notice as they age, with pigmented hairs often darkening from brown toward black before eventually going grey.5PubMed Central. Morphological changes in hair melanosomes by aging
Because the melanosomes are embedded within the cortex rather than sitting on the surface, hair color is an intrinsic property of the fiber’s interior. Damage to the cuticle can make hair look duller or more faded because light enters and scatters differently, but the actual pigment is deeper inside.
How Greying Happens Inside the Cortex
Grey and white hairs are not actually “grey” in the way paint is grey. They are hairs whose cortex contains little to no melanin. The melanocytes at the base of the follicle gradually lose their ability to produce pigment, and the cortical cells that form afterward are essentially colorless. A mix of fully pigmented and unpigmented hairs on the same head creates the salt-and-pepper appearance that people describe as “going grey.”
A key area of research into greying focuses on the melanocyte stem cell compartment in the hair follicle. The current understanding is that these stem cells become depleted over time, likely driven in part by damage from reactive oxygen species combined with a decline in the follicle’s antioxidant defenses and a failure of the stem cells to properly renew themselves.6PubMed Central. Aging of the hair follicle pigmentation system Once the stem cell reservoir is exhausted for a given follicle, every hair it produces from that point on will be unpigmented. The keratin structure of the cortex itself remains largely the same in grey hair; it is the absence of melanosomes that changes the appearance.
What Happens When the Cortex Gets Wet
Hair absorbs water, and the cortex is where most of that absorption takes place. When you step out of the shower, each strand has swelled in diameter and increased in length slightly. The cuticle absorbs some moisture, but the cortex, with its massive volume of keratin and associated proteins, is the main reservoir.
Recent work using atomic force microscopy on hair cross-sections at different humidity levels has allowed researchers to watch the cortex and cuticle swell in real time, tracking changes in the dimensions of individual cortical cells and cuticle layers as relative humidity increases.7PubMed. New insights into hair compartments swelling via atomic force microscopy and dynamic vapour sorption Separate measurements of moisture sorption kinetics have shown that the cortex and cuticle absorb water at different rates, and that the entanglement of protein chains within each compartment influences how quickly and how much each layer swells.8PubMed. The kinetics of moisture sorption by hair
This swelling matters for everyday hair care. When the cortex swells, it pushes outward against the cuticle, which can cause cuticle scales to lift and separate. Repeated swelling and drying cycles, such as washing and blow-drying every day, gradually wear down the cuticle and expose the cortex to further damage. It is also why hair is weaker and more elastic when wet: the water disrupts the hydrogen bonds inside the cortex that normally contribute to stiffness, leaving the fiber more pliable and more vulnerable to mechanical breakage.
How Bleaching and Chemical Treatments Attack the Cortex
Bleaching is one of the most aggressive things you can do to the cortex. The bleaching agent, typically hydrogen peroxide combined with an alkaline booster, penetrates through the cuticle and enters the cortex where it destroys melanin granules and breaks disulfide bonds. Microscopic analysis of bleached hair shows that the cuticle layer separates from the cortex, and numerous pores form within the cortex where melanin granules once sat, scattered between the macrofibrils. No melanin granules remain detectable in heavily bleached cortex, though the macrofibril structure can stay largely intact.9PubMed Central. Effects of excessive bleaching on hair: comparative analysis of external morphology and internal microstructure
The chemical damage goes beyond just dissolving pigment. Proteomic studies of bleached hair have found that the proteins leached out during bleaching are not limited to the cuticle but also include cortical intermediate filaments and matrix keratin-associated proteins. The protein oxidation that occurs targets sulfur-containing amino acids especially hard, converting the cystine disulfide bonds into cysteic acid. Even the mildest bleach treatment can cause extensive melanin granule degradation.10PubMed. The physical and chemical disruption of human hair after bleaching – studies by transmission electron microscopy and redox proteomics Once disulfide bonds have been oxidized to cysteic acid, they cannot be reformed; the damage is permanent. This is why repeated bleaching leads to progressively weaker, more porous, and more brittle hair. Conditioning treatments can temporarily fill in surface damage and improve the feel of the hair, but they cannot rebuild the cortex’s internal cross-links.
Sun Exposure and Heat Damage
Ultraviolet light and high heat from styling tools also degrade the cortex, though usually more gradually than chemical treatments. UV exposure triggers a cascade of changes in the fiber: lipids on and within the hair oxidize, disulfide bonds break, and the amino acid tryptophan degrades. The cumulative result is increased porosity, loss of mechanical strength, and a rougher surface.11PubMed Central. Photoaggravation of hair aging
Tryptophan plays a particularly interesting role. It absorbs UV light and, in doing so, transfers energy to nearby disulfide bonds, disrupting them. Researchers tracking fluorescence changes in UV-exposed hair have documented progressive tryptophan degradation with each exposure, providing evidence that the damage accumulates. Each round of UV exposure chips away at a few more disulfide bridges in the cortex, gradually weakening the fiber’s structural integrity.12Advances in Bioscience and Biotechnology. Changes in Human Hair Induced by UV- and Gamma Irradiation This is distinct from the mechanism of gamma radiation damage, which acts through free radicals and direct energy deposition rather than the tryptophan pathway. For practical purposes, the UV damage mechanism explains why hair that gets heavy sun exposure, particularly along the part line or around the hairline, tends to lighten in color and feel drier and more fragile over time, even without any chemical treatments.
Heat styling operates on a simpler principle. Flat irons and curling irons applied at high temperatures essentially cook the keratin proteins in the cortex. At moderate temperatures, the heat breaks hydrogen bonds and allows temporary reshaping. At higher temperatures, typically above about 230°C (around 450°F), proteins begin to denature more permanently, and moisture trapped inside the cortex can flash to steam, creating micro-bubbles within the fiber that weaken it from the inside out.
How the Cortex Forms in the First Place
The cortex is built from scratch during each hair growth cycle in the hair follicle, specifically in the bulb region at the very base of the follicle. Here, rapidly dividing cells sit near a cluster of signaling cells called the dermal papilla. As these cells divide and begin to differentiate, different cell streams are programmed to become the cuticle, the cortex, the inner root sheath, or the medulla.
In cells destined to become the cortex, a specific family of keratin genes is activated in a sequential pattern. Type II keratin intermediate filament genes, which are among the earliest markers of cortical cell identity, are first switched on in cells located in the middle of the bulb near the dermal papilla. As these cells migrate upward through the follicle, additional keratin genes are activated, and the cells accumulate more and more keratin protein until they are fully keratinized, meaning they are essentially dead, rigid, protein-packed structures by the time they emerge from the scalp.13PubMed. Hair follicle differentiation: expression, structure and evolutionary conservation of the hair type II keratin intermediate filament gene family Importantly, these cortex-specific keratin genes are not expressed in the cells that form the outer root sheath, the inner root sheath, or the medulla, confirming that the cortex is a distinctly programmed tissue within the follicle.
This process repeats roughly every growth cycle, which in scalp hair typically lasts several years. Each time, the cortex is rebuilt from new cells, which is why damage to existing hair cannot be “healed” by the body. The living part of the hair exists only deep inside the follicle. Everything above the scalp is already dead tissue, and any damage to the cortex from that point on is permanent unless the damaged section is cut off and replaced by new growth.
The Evolutionary Story of Cortex Proteins
The keratin and keratin-associated proteins that make up the cortex are not unique to humans. All mammals have hair built on fundamentally the same cortical architecture, though the specific protein composition varies between species and accounts for the enormous diversity of mammalian hair types, from the coarse quills of a porcupine to the fine underfur of a mink.
Genomic studies of the keratin-associated protein (KRTAP) gene family across mammals have found that most KRTAP subfamilies emerged early in mammalian evolution, suggesting that the common ancestor of all mammals already had a diverse set of these genes. The research indicates that KRTAP genes have evolved and diverged rapidly between species, which likely explains why hair characteristics differ so much across the mammalian family tree. At the same time, within any given species, these gene subfamilies have been homogenized through a process called concerted evolution, meaning the copies within one species tend to stay similar to each other even as they diverge from the copies in other species.14PubMed Central. Molecular evolution of the keratin associated protein gene family in mammals, role in the evolution of mammalian hair
This pattern of rapid evolution between species and homogenization within species helps explain a puzzle that anyone who has ever owned both a cat and a dog might appreciate: why different mammals’ hair feels, behaves, and responds to the environment so differently despite being built on the same basic cortical blueprint. The cortex is an ancient structure, conserved in its general plan for over a hundred million years, but fine-tuned at the molecular level in every lineage that has inherited it.
Environmental Pollutants and the Hair Follicle
Beyond the cosmetic and physical stresses most people think about, environmental pollutants can affect the hair at the level of the follicle itself, potentially disrupting cortex formation before the hair even emerges. Research has linked exposure to pesticides and heavy metals with conditions like alopecia areata (patchy hair loss driven by immune attack on the follicle) and acute anagen effluvium (sudden shedding of actively growing hairs). Polyaromatic hydrocarbons, which act on specific cellular receptors, have been connected to androgenetic alopecia, the pattern hair loss that affects both men and women.15PubMed Central. The Effects of Environmental Pollutants and Exposures on Hair Follicle Pathophysiology While most discussions of cortex health focus on what happens to the hair shaft after it has grown, these findings suggest that the cortex’s quality and integrity can be compromised from the very start if the follicle environment is disturbed by external toxins.