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Objective To assess the views of men who have sex with men (MSM) and transgender women (TGW) on acceptability of using meatal swabs compared with first-catch urine (FCU), and acceptability and accuracy of pooling three-site samples compared with individually analysed samples, for gonorrhoea and chlamydia detection, using a questionnaire.Methods Prospective, convenience, sample of MSM/TGW attending UK sexual health clinic. Randomised order of self-taken samples from the pharynx and rectum, plus self-taken penile-meatal swab and FCU, for gonorrhoea and chlamydia detection. Participants were then asked to complete a questionnaire on acceptability and ease of taking the meatal swabs compared with FCU samples, and the pooling processes compared with individual samples.Results Questionnaire completion was 426/432 (98.6%) of participants offered it. Over 90% reported: finding written instructions and diagrams about taking the meatal swab clear and easy to follow; feeling confident about taking the meatal swab; finding written instructions and diagrams of how to pool the samples clear and easy to follow; and being confident about pooling the samples.When asked ‘If the pooled sample with the meatal swab was the same at finding chlamydia as the pooled sample with the urine’ 50% would prefer the meatal swab, 42% preferred urine and 8% had no preference. When asked ‘If the pooled sample with the meatal swab was better at finding chlamydia than the pooled sample with the urine’ 86% would prefer the meatal swab, 12% preferred urine and 2% had no preference.Conclusions In this first study to assess people’s views of taking their own penile-meatal swab versus FCU, the MSM/TGW participants found taking meatal swabs was easy and acceptable and a small majority preferred them to FCU even if no improved diagnostic sensitivity over urine. These results challenge the conventional thinking that urine is the preferred urogenital sample in MSM/TGW.