The aim of our study was to look at the overall risk of peritonitis post colonoscopy in end stage renal disease patients on automated peritoneal dialysis and to evaluate the use of prophylactic antibiotic in those patients when given prior to colonoscopy. A total of 93 patients out of 134 patients on automated peritoneal dialysis (APD) undergoing diagnostic colonoscopy were enrolled in a prospective randomized study. The study extended from January 2016 throughout May 2018 Patients were randomized into two age and sex matched groups; group 1 (46 patients) who had prophylaxis ceftazidime prior to colonoscopy and group 2 (47 patients) who had colonoscopy without prophylactic antibiotics. The following parameters: age, gender, duration on dialysis, duration on APD, diabetic status, use of antibiotics before the procedure, and indications for and findings of colonoscopy were studied. Prophylactic antibiotics were given for prevention of peritonitis if needed according to the 2010 ISPD guidelines. Results: Post-colonoscopy peritonitis was documented in 2 (4.3%) and 3 (6.4%) patients in groups A and B respectively (p > 0.05). The most common causative agents were gram negative bacteria and there were no other complications. Conclusion: There was no strong correlation between prophylactic antibiotic use and risk of peritonitis in peritoneal dialysis patients and it seems that the overall risk of developing peritonitis after colonoscopy is low. Only old age, diabetes mellitus and low serum albumin appear to be of significance. Polypectomy; partial or complete did not increase peritonitis episodes in our study population.