The detection of a sexually transmitted infection (STI) agent in a urine specimen from a young child is often regarded as a strong indicator of sexual abuse. However, the parameter of key medico-legal significance is the positive predictive value (PPV) for abuse of a positive STI test. The low sensitivity of STI diagnosis for detecting abuse, and the potential low prevalence of abuse, mean that the PPV can be extremely sensitive to the frequency of positive STI tests in the absence of abuse. Such frequencies are not well understood. False positives may arise from the transfer of environmental contaminants in clinic toilet/bathroom facilities into urine specimens.  This was tested empirically in ten Northern Territory Clinic toilet-bathrooms. Each was visited seven times. At each visit, the extent of environmental contamination with Chlamydia trachomatis, Neisseria gonorrhoeae and Trichomanas vaginalis nucleic acid was determined. In addition, the process of urine collection was simulated using a synthetic urine surrogate. This procedure encompassed contact between the gloved hands and the environment and gloved hands and the inside of the urine collection jar lid. The urine surrogate samples were tested for STI nucleic acids. The most contaminated toilet-bathrooms were in remote Indigenous communities. No contamination was found in the Northern Territory Government Sexual Assault Referral Centre clinics, and intermediate levels of contamination were found in sexual health clinics, and clinics in regional urban centres. In general, T. vaginalis was the most abundant contaminant, and C. trachomatis the least abundant. The frequency of surrogate urine sample contamination was low but non-zero. For example, of the 4/558 (0.7%) of the urine surrogate specimens from remote clinics were STI positive. This frequency represents a conservative estimate of the upper limit for the STI test false positive frequency for urine specimens obtained in STI nucleic acid-contaminated environments.