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A self versus clinician Chlamydia/gonorrhoea (CT/NG) NAAT swab trial, with pooling of self-taken samples, recruited January 2015–September 2016. There was concern that nucleic acid contamination of clinic surfaces could be a source of false-positive samples during the pooling process.To ascertain levels of environmental nucleic acid contamination within clinic environments. To determine number of false positive pooled samples throughout study.Environmental samples of clinic rooms, sluices and toilets were performed and tested using Aptima Combo 2 throughout duration of study. In November 2015, the clinic relocated from old premises to a newly renovated site.Results were disseminated to staff throughout to raise awareness and to reduce risk of contamination during sampling/pooling. Posters in self-swab areas highlighted risk of contamination, importance of handwashing and no surface contact for swabs.Of 41 environmental sampling episodes over 12 months, 17 (41%) were CT/GC positive/indeterminate. These were distributed throughout the whole 12 months. Positive results were obtained from surfaces in all clinical examination rooms at the old site and toilets and sluices (where urines were pipetted) at both sites. 3/4 clinic rooms regularly used for examination at the new site remained contamination free. There were 7 false positive pooled samples (6 female, 1 male); all were in the first 6-months of the study.Nucleic acid contamination was repeatedly found throughout the clinic despite regular cleaning/decontamination. Raising staff and patient awareness did not reduce contamination but it did reduce false positive pooled samples, with none occurring after the first 6-months.