Snakes do not have a penis in the mammalian sense. Instead, male snakes have a pair of reproductive organs called hemipenes, stored internally at the base of the tail and used one at a time during mating. These structures are fundamentally different from a mammalian penis in how they develop, how they work, and even where they come from embryologically. The story of hemipenes touches on evolutionary puzzles, sexual arms races, and a recently discovered female counterpart that researchers had overlooked for centuries.
Two Instead of One
Male snakes carry a fully independent reproductive system on each side of the body, including a testis, a sperm duct, and a hemipenis. Each hemipenis sits inverted inside a pocket called the hemipenial sheath, located just behind the cloaca (the single opening snakes use for waste and reproduction). During mating, only one hemipenis is deployed at a time. A study of garter snakes found that overall hemipenis usage averaged close to 50/50 between the left and right organs, though individual males tended to alternate sides in successive matings, possibly because the glandular material used to form a mating plug gets temporarily depleted on one side.1Behavioral Ecology. Are snakes right-handed? Asymmetry in hemipenis size and usage in gartersnakes (Thamnophis sirtalis)
The hemipenis does not work like a mammalian penis, which fills with blood inside a permanently external structure. Instead, a hemipenis is turned inside out, like peeling off a glove finger, when blood pressure forces it to evert through the cloacal opening. The smooth muscle surrounding the organ relaxes to allow expansion, and radial muscle bundles act as internal struts to control how far and how fast the organ inflates. Once mating is complete and blood pressure drops, a retractor muscle pulls the hemipenis back inside, inverting it into its resting position again.2PLOS ONE. The Evolutionary Implications of Hemipenial Morphology of Rattlesnake Crotalus durissus terrificus (Laurent, 1768) (Serpentes: Viperidae: Crotalinae)
Spines, Hooks, and Surface Ornamentation
If you have ever seen a photograph of an everted hemipenis, the first thing you probably noticed is how alien it looks. The outer surface can be covered in an elaborate array of ridges, cups (called chalices), flounces, and calcified spines or hooks.3PubMed Central. Evolutionary morphology of genital spines informed by puncture mechanics These features are not decorative. Some of the more heavily ornamented hemipenes appear to function as locking devices that anchor the organ inside the female’s cloaca during copulation, which in some species can last for hours.4PubMed. Does Sexual Selection Influence Ornamentation of Hemipenes in Old World Snakes?
The spines are not equally developed in all species. Some snakes have smooth or lightly ridged hemipenes, while others sport an armory of mineralized hooks. The degree of ornamentation varies not just between species but sometimes between populations of the same species, a fact that has made hemipenis shape a useful tool for taxonomists trying to tell closely related snakes apart. Intraspecific variation in hemipenis shape is common in geographically widespread species and sometimes signals the existence of unnamed cryptic species that look alike externally but differ in genital morphology.5Bulletin of the American Museum of Natural History. New Taxa and Cryptic Species of Neotropical Snakes (Xenodontinae), with Commentary on Hemipenes as Generic and Specific Characters
How Sperm Actually Gets Where It Needs to Go
A hemipenis has no internal tube for sperm. Unlike a mammalian penis with its enclosed urethra, the hemipenis carries sperm along an external groove on its surface called the sulcus spermaticus. This groove typically runs along the length of the everted organ and splits into two branches near the tip.6Oxford Academic. Comparative Aspects of the Hemipenial Architecture of the Arabian Horned Viper Cerastes gasperettii: Macroscopic and Microscopic Analysis With Evolutionary Perspectives When the hemipenis is inserted into the female’s cloaca, sperm flows along this open channel to reach the oviducts. It is a fundamentally different plumbing design from what mammals use, and it reflects the fact that hemipenes evolved along a separate path.
Copulatory Plugs and Mate Guarding
In several snake species, the male leaves behind more than just sperm. Immediately after insemination, secretions from the kidney form a copulatory plug that blocks the oviductal openings of the female’s cloaca for several days. The plug functions as a form of enforced chastity, making it difficult for rival males to mate with the same female during the window when her eggs are being fertilized.7PubMed. Copulatory plugs in snakes: enforced chastity This is part of why garter snake males appear to alternate hemipenes between matings: the plug material on one side needs time to regenerate.1Behavioral Ecology. Are snakes right-handed? Asymmetry in hemipenis size and usage in gartersnakes (Thamnophis sirtalis)
Copulatory plugs are one piece of a broader sexual conflict playing out across snake species. Researchers studying watersnakes have documented variation in female reproductive tract morphology between closely related species, raising the question of whether female anatomy has coevolved with male genital shape. If male hemipenis ornamentation acts as a locking mechanism, female tract morphology may have evolved partly in response, potentially creating mechanical barriers that contribute to reproductive isolation between species living in the same area.8Biological Journal of the Linnean Society. Intraspecific and interspecific variation of female genitalia in two species of watersnake
The Female Counterpart That Was Overlooked for Centuries
For a long time, discussions of snake reproductive anatomy focused exclusively on males. That changed in 2022 when researchers published the first complete description of hemiclitores in female snakes, examining nine species across four families. The snake hemiclitores are a pair of small, triangular structures located in the same region as the male hemipenes. Unlike hemipenes, hemiclitores are non-eversible; they stay inside the body. Histological examination revealed that they contain erectile tissue and nerve bundles but lack the spines found on male hemipenes.9PubMed Central. First evidence of hemiclitores in snakes
The discovery was significant for several reasons. Previous researchers who noticed these structures had either dismissed them as underdeveloped hemipenes (suggesting the snake was an intersex individual) or mistaken them for scent glands. The nerve-rich, erectile tissue in the hemiclitores suggests they play a functional role during mating, possibly in stimulation or signaling. Radiographic comparisons between hemipenes and hemiclitores in golden lancehead vipers showed that hemipenes appear as herringbone-shaped structures with bone-like density, while hemiclitores appear as softer, triangular structures, confirming that the spines of hemiclitores do not reach the same level of mineralization as those of hemipenes.10PubMed. Morphological and structural differences between the hemipenes and hemiclitores of golden lancehead snakes, Bothrops insularis (Amaral, 1922), revealed by radiography The two structures share an anatomical position and a paired layout, but they are clearly distinct organs.
Not Really a Penis at All
One of the more surprising findings in reptile reproductive biology is that snake hemipenes may not be direct evolutionary relatives of the mammalian penis. In mammals and birds, external genitalia develop from paired swellings that appear on the front side of the cloaca and then fuse into a single structure. Snake hemipenes, by contrast, develop from paired swellings on the sides of the cloaca and never fuse. Research on ball python embryos showed that hemipenes lack an endodermal contribution (the inner tissue layer that forms the urethral lining in mammals), and the signaling gene Sonic hedgehog, which is critical for mammalian genital outgrowth, does not appear in the hemipenis sulcus.11PubMed. Development of hemipenes in the ball python snake Python regius
These differences raise the possibility that hemipenes arose independently from the single penis found in mammals, birds, and crocodilians. Yet the picture is not that simple. Some of the same developmental genes are expressed in both snake hemipenis buds and mammalian genital tubercles, hinting that while the structures themselves may have evolved separately, they draw on an ancient shared genetic toolkit. Work in lizards found that at early developmental stages, the hemipenis transcriptome is virtually indistinguishable from a limb molecular signature, and only later differentiates into a genital identity.12Nature. A relative shift in cloacal location repositions external genitalia in amniote evolution In squamates, genitalia develop from cells that would otherwise build hindlimbs, whereas in mammals the genital tissue comes from a different cell population near the tail. The difference traces back to a shift in the position of the cloaca during evolution, which redirected genital-inducing signals to a new target tissue.
A complementary line of evidence comes from tuatara embryos. Adult tuataras lack any intromittent organ entirely, yet their embryos develop genital swellings at an early stage before the structures regress. This suggests that external genitalia have a single deep evolutionary origin across all amniotes, even when the resulting organs look very different or are lost altogether in adults.13PubMed Central. Resurrecting embryos of the tuatara, Sphenodon punctatus, to resolve vertebrate phallus evolution
How to Tell a Male Snake from a Female
Because hemipenes are stored internally, you cannot sex a snake just by looking at its underside. The most common field and veterinary method is probing: a smooth, lubricated rod is gently inserted into one of the hemipenial pockets at the base of the tail. In males, the probe slides into a deeper cavity because the inverted hemipenis creates a longer pocket. A study of reticulated pythons found that the probe typically reached about 1 to 3 centimeters deep in males, while in females it could only be inserted less than 0.8 centimeters, since females lack hemipenes and have only small vestigial pockets (scent gland openings).14BIOTROPIA. Comparative Analysis of Probing and Contrast Radiography for Gender Determination in Reticulated Pythons (Malayopython reticulatus)
Probing is reliable when done by experienced handlers, but it carries a risk of injuring the animal if performed carelessly, particularly in small or juvenile snakes. An alternative approach involves contrast radiography, where a contrast agent is injected near the hemipenial area and X-rays reveal whether hemipenes are present. The same reticulated python study found that probing was more consistently accurate than contrast radiography, which occasionally produced false-positive results.14BIOTROPIA. Comparative Analysis of Probing and Contrast Radiography for Gender Determination in Reticulated Pythons (Malayopython reticulatus) For very young snakes, a gentler technique called “popping” is sometimes used, where light pressure at the base of the tail briefly everts the hemipenes in males. This works best in neonates and small juveniles and becomes less reliable as the animal grows.
When Things Go Wrong
Hemipenis prolapse is one of the more common reproductive emergencies seen in captive snakes. The organ everts and cannot retract, leaving it exposed and vulnerable to swelling, drying out, and infection. Causes include prolonged mating attempts, handling during mating season, infections, constipation, and neurological problems affecting the retractor muscle. If a prolapsed hemipenis is treated quickly, a veterinarian can often reduce the swelling and manually replace it. When the tissue has been exposed too long and becomes necrotic, surgical amputation of the affected hemipenis is sometimes necessary. Because snakes have two hemipenes, losing one does not make the animal infertile; the remaining organ on the other side still functions normally.
Distinguishing a hemipenis prolapse from a cloacal prolapse of other tissue (intestine or oviduct) is an important diagnostic step, since the treatments differ. The presence of the sulcus spermaticus groove on the everted tissue is a reliable indicator that the protruding organ is a hemipenis rather than intestinal tissue.
Why Hemipenis Shape Matters for Identifying Species
Herpetologists have relied on hemipenis morphology for species identification since the 19th century, and the practice remains important today. Two snake species can look nearly identical in color, scale count, and body proportions while having strikingly different hemipenes. This makes hemipenis shape one of the most reliable anatomical characters for distinguishing cryptic species that would otherwise be lumped together. In a major revision of neotropical xenodontine snakes, researchers used hemipenial characters extensively and noted that geographic variation in hemipenis shape within widespread species sometimes flagged the presence of separate, previously unnamed species.5Bulletin of the American Museum of Natural History. New Taxa and Cryptic Species of Neotropical Snakes (Xenodontinae), with Commentary on Hemipenes as Generic and Specific Characters
The usefulness of hemipenes in taxonomy does have limits. Not every population-level difference in hemipenis shape reflects a species boundary. Geographic variation is common, and deciding when that variation crosses the line into species-level distinction requires additional evidence from genetics and ecology. Still, when a field researcher encounters a snake that looks familiar but whose hemipenis is shaped nothing like the known species in the area, it is a strong hint that something taxonomically interesting is going on.
Lizards Have Them Too
Hemipenes are not unique to snakes. All squamate reptiles, the group that includes snakes, lizards, and amphisbaenians (worm lizards), possess paired hemipenes. The shared anatomy reflects the close evolutionary relationship between snakes and lizards, with snakes essentially being highly modified, limbless lizards. The developmental connection between limbs and genitalia in squamates reinforces this: the same cell populations that build legs in a lizard contribute to hemipenis formation, and in snakes, which lost their legs long ago, those cell remnants still give rise to hemipenes.12Nature. A relative shift in cloacal location repositions external genitalia in amniote evolution It is a striking example of how evolution repurposes the same raw materials for different functions depending on the body plan.
Other reptile groups took a different path. Crocodilians and turtles have a single, unpaired penis, more structurally similar in some ways to the mammalian organ. Birds, which are the living descendants of dinosaurs, mostly lost external genitalia entirely, with the notable exception of ducks and a few other waterfowl that retain a phallus. The squamate solution of keeping two separate organs and using them one at a time is, as far as vertebrates go, unusual, and the evolutionary pressures that maintained it likely have to do with the paired structure being advantageous for species where mating involves rapid alternation or competition between males at a breeding site.