The aim of this study was to assess if patient characteristics could influence the sensitivity of enzyme immunoassay (EIA) testing used for chlamydia screening. Our cohort consisted of 56 patients who were known polymerase chain reaction-positive for chlamydia, but with variable EIA results. Characteristics analysed included those already known to influence the EIA (menstruation, pregnancy, difficult examination) and those suspected from clinical observation (including presence of symptoms or signs, coexistent gonorrhoea, duration from last sexual exposure). An unexpected finding was that significantly more cases of bacterial vaginosis were found in those chlamydia EIA-negative compared to those with positive results. We postulate that an enzyme produced in bacterial vaginosis, proline aminopeptidase, may cause destruction of the chlamydial cell wall, therefore affecting the EIA adversely. Further research is needed to explore this hypothesis.