BACKGROUND: Sexually transmitted infections (STIs) are a global health challenge. Testing is not routinely performed in low- and middle-income countries (LMICs), which bear a disproportionate burden of STIs. Self-collected penile-meatal swabs (SCPMS) are an alternative to urine for STI testing, but data from LMICs are limited. METHODS: Between October 2019 and September 2020, recruited participants with urethral discharge syndrome at government health facilities in Kampala, Uganda, provided urine and SCPMS. Samples were retrospectively analysed for RESULTS: Of the 250 participants, 66.8% (n=167), 22.8% (n=57), 12.8% (n=32) and 2.4% (n=6) tested positive for NG, CT, MG and TV, respectively, on testing of their SCPMS and urine samples. The overall agreement between urine and SCPMS for all STIs using the Aptima assays was 98.7% (987/1000). After adjudication with PCR assays, the agreement between urine and SCPMS for NG, CT, MG and TV was 100% (250/250), 97.6% (244/250), 99.6% (249/250), and 99.6% (249/250), respectively. There was no significant difference between SCPMS and urine (p=0.9996). For paired samples with one STI (n=164) or ≥2 STIs (n=39), concordance was 100% (656/656) and 97.2% (175/180), respectively. There was no association between number of STIs and agreement between sample types (p=0.8606). CONCLUSIONS: This study revealed a high level of agreement between SCPMS and urine for detection of STIs in symptomatic Ugandan men, even in the presence of multiple concurrent STIs. SCPMS may be a suitable alternative to urine, with ease of collection, transporting, and processing of samples.