Colonoscopy is one of the safest procedures in medicine, but it does carry real risks. Serious complications like bleeding or a tear in the bowel wall occur in fewer than 1 in 100 procedures, and the death rate is roughly 3 per 100,000 colonoscopies. Most people walk away with nothing worse than temporary bloating. Still, knowing what can go wrong helps you recognize warning signs and have a more informed conversation with your doctor beforehand.
Bleeding During or After the Procedure
Bleeding is the most common complication, especially when polyps are removed. In screening colonoscopies, about 0.3% of patients experience confirmed bleeding either during or within four weeks of the procedure. When polyps are removed, the rate of immediate bleeding rises to around 2.8%. That bleeding is usually spotted and controlled on the spot.
Delayed bleeding is the version that catches people off guard. It happens in 0.2% to 2.2% of polypectomy cases and can show up anywhere from 24 hours to three weeks later. You might notice blood in your stool, feel lightheaded, or pass dark, tarry stools. Most delayed bleeds stop on their own or can be treated with a follow-up endoscopy, but heavy or persistent bleeding needs prompt medical attention.
Perforation of the Bowel Wall
A perforation, or tear, in the colon is the complication doctors worry about most. It happens in 0.016% to 0.2% of diagnostic colonoscopies. When therapeutic work is involved, like removing large polyps or dilating a narrowed section, the rate can climb as high as 5% for certain interventions.
There are a few ways this can happen. The shaft of the scope can overstretch the colon wall, particularly when it forms a loop in the sigmoid colon. This tends to produce a larger tear. The tip of the scope can also cause a smaller puncture. During polyp removal, electrical current used to cut tissue can cause a thermal injury that burns through the full thickness of the bowel wall. Symptoms of perforation include severe abdominal pain, fever, a rigid abdomen, and rapid heart rate. These usually appear within hours but can be delayed. A perforation often requires hospitalization and sometimes surgery.
Post-Polypectomy Syndrome
This is a close cousin of perforation that mimics its symptoms but is less dangerous. It happens when the electrical current used during polyp removal burns the bowel wall deeply without actually creating a hole. Patients typically develop fever, abdominal pain, and a fast heart rate within 12 hours of the procedure, though symptoms can be delayed by up to five to seven days. The good news is that it usually resolves on its own within two to five days with rest and observation. The tricky part is distinguishing it from a true perforation, which is why imaging is often needed.
Sedation-Related Problems
Cardiopulmonary complications are actually the most common adverse events that happen during the procedure itself. The sedation drugs used to keep you comfortable can temporarily affect your breathing and blood pressure.
A large meta-analysis of sedation with propofol (the most widely used sedation drug for colonoscopy) found that about 4 in 100 patients experience a drop in oxygen levels, and roughly the same proportion experience a temporary dip in blood pressure. A slow heart rate occurs in about 1 in 100. Severe drops in oxygen saturation are much rarer, affecting about 6 in 1,000 patients. These events are typically brief because the medical team monitors your vitals continuously and can intervene within seconds, adjusting oxygen flow or medication as needed.
People with heart disease, lung conditions, or obesity face a higher risk from sedation. If you have sleep apnea or chronic lung disease, mention it during your pre-procedure consultation so the team can adjust their approach.
Infection After the Procedure
Infection is uncommon but not as rare as once thought. A large study of ambulatory surgery centers found a rate of about 1.1 infections per 1,000 screening colonoscopies, and 1.6 per 1,000 for non-screening colonoscopies. These are bacterial infections that can develop within the first week. The risk varies widely by facility, which underscores the importance of choosing a center with strong reprocessing protocols for its equipment. Infections linked to improperly cleaned scopes have made headlines, though they remain rare overall.
Splenic Injury
The spleen sits near the bend where the colon curves under the left rib cage, and the scope can occasionally tug on tissue that connects to it. Splenic injury after colonoscopy is rare, with only about 73 cases reported in the medical literature, but it can be life-threatening. Around 22% of reported cases involved a full splenic rupture, while the rest were smaller injuries like blood collections beneath the spleen’s outer lining.
The hallmark symptom is worsening pain in the upper left part of your abdomen, sometimes accompanied by nausea, dizziness, or pain radiating to the left shoulder. Symptoms can begin within a few hours of the procedure. This is easy to dismiss as normal post-procedure gas pain, but left upper quadrant pain that intensifies rather than fading is a red flag worth taking seriously.
Risks From the Bowel Preparation
The prep itself carries its own set of risks, particularly for older adults and people with kidney, heart, or liver conditions. The large-volume liquid laxatives pull fluid into the gut to flush it clean, and this fluid shift can throw off your body’s electrolyte balance.
A systematic review found that sodium phosphate-based preps caused elevated phosphate levels in over 37% of patients and low calcium in nearly 16%. The more commonly used polyethylene glycol preps are gentler on electrolytes overall but still caused low sodium levels in about 3.3% of patients. For most healthy adults, these shifts are temporary and cause no symptoms. For people with kidney problems or those on certain blood pressure medications, the same shifts can be clinically significant. This is one reason your doctor asks about your medical history before prescribing a specific prep formula.
Missed Findings
A complication of a different kind is a false sense of security. Colonoscopy is the gold standard for detecting colon polyps and cancer, but it is not perfect. Back-to-back colonoscopy studies, where the same patient gets scoped twice in one session, have shown that about 17% of adenomas (precancerous polyps) are missed on the first pass. For advanced adenomas, the ones most likely to progress to cancer, the miss rate drops to about 5.4%. Small and flat polyps in hard-to-visualize folds are the usual culprits.
This is why adherence to recommended screening intervals matters. A missed polyp at your current colonoscopy has a chance of being caught at your next one, long before it becomes dangerous.
Who Faces Higher Risk
Age is the single biggest modifier. Patients over 80 have higher rates of perforation, bleeding, and incomplete procedures compared to younger adults, with overall major complication rates between 0.2% and 0.6%. They are also more likely to have poor bowel preparation because drinking four liters of prep solution is a significant challenge, and kidney or heart conditions may limit which prep formulas are safe to use.
Longer and more complex procedures also raise the stakes. A straightforward screening colonoscopy in a healthy 55-year-old carries far less risk than a therapeutic colonoscopy involving multiple large polyp removals in a patient with heart failure. The presence of existing conditions, particularly cardiovascular disease, chronic lung disease, and kidney impairment, amplifies both procedural and sedation-related risks. Your doctor should weigh these factors when deciding whether the benefits of the procedure outweigh the potential harms, especially for elective screenings in older or sicker patients.