Objectives Pelvic inflammatory disease (PID) occurs when pathogens, often sexually transmitted, ascend to the upper genital tract, yet a causative pathogen is not detected in a substantial proportion of diagnosed PID. We assessed the characteristics associated with PID in women in whom chlamydia, gonorrhoea, Mycoplasma genitalium (MG) and bacterial vaginosis (BV) were not detected ('pathogen-negative-PID'). Methods Cross-sectional analysis of routinely collected clinical data from new female patients attending a sexual health clinic between 2006 and 2013. Women were eligible if they had been diagnosed with PID and tested for genital chlamydia, gonorrhoea, MG and BV. Logistic regression was conducted to identify characteristics associated with pathogen-negative-PID. Results Among 330 women with clinically diagnosed PID, 204 (61.8%, 95% CI 56.3% to 67.1%) had pathogen-negative-PID. Compared with pathogenpositive- PID, pathogen-negative-PID cases were more likely to be aged =30 years (adjusted odds ratio (AOR) 1.7, 95% CI 1.0 to 3.0), had less evidence of vaginal inflammation (AOR 0.5, 95% CI 0.3 to 0.9) and reported less unprotected sex (AOR 0.6, 95% CI 0.4 to 1.0). Conclusions These findings highlight uncertainties around PID diagnosis and aetiology. Pathogen-negative- PID could represent (i) a false positive diagnosis where the woman does not have a sexually transmitted infection (STI) or PID, (ii) PID of another microbiological aetiology or associated with a past STI or (iii) PID where the cervical infection has cleared. However, until diagnostic biomarkers are available, PID treatment should be based on clinical features and sexual risk.