Trials on cap-assisted colonoscopy have shown a reduction in pain, faster intubation time and a higher success rate attributed to the use of the cap. No similar studies have been published on sigmoidoscopy even though it is a common procedure associated with significant pain. Our objective was to investigate whether the use of a transparent cap for sigmoidoscopy has an impact on pain, time or success rate. To mimic the tendencies of daily clinical practice, the trainee endoscopist performed the procedures, and no analgesics or sedatives were used. We conducted a randomized, controlled clinical trial with a parallel design consisting of two groups masked for the intervention. The primary endpoint was pain, recorded on a 100-mm visual analogue scale (VAS). Our results found cap-assisted sigmoidoscopy to be significantly more painful than non-cap-assisted sigmoidoscopy (median VAS 50 vs. 38 mm; p = 0.047). We found no differences on time or success rate due to the cap. Our results suggest pain management, e.g. analgesics which is not routinely used for sigmoidoscopy, when a cap is used to gain therapeutic or diagnostic advantages. ClinicalTrials.gov Identifier: NCT02243930.