Background: To determine if female partners of men with pathogennegative non-gonococcal urethritis (NGU) are at risk of genital infection. Methods: Secondary data analysis using health records from a large sexually transmitted disease clinic inMelbourne of 1710 men and their female partners attending on the same day from January 2006 to April 2015. Proportions of female partners with symptoms suggesting genital infection or pelvic inflammatory disease (PID) were determined for: (1) men with NGU and no Chlamydia trachomatis or Mycoplasma genitalium (referred to as pathogen-negative NGU) (n = 91); 2) men with urethral C. trachomatis (n = 176); 3) men with urethral M. genitalium (n = 26); and 4) asymptomatic men (n = 652). Results: Female partners of men with pathogen-negative NGU experienced deep pelvic pain (adjusted odds ratio [AOR], 2.2; 95% confidence interval [CI], 1.1-4.4), post coital bleeding (AOR, 2.4; 95% CI, 1.2-4.9), and dysuria (AOR, 3.7; 95% CI, 1.6-8.6) more commonly and were diagnosed with PID more commonly (AOR, 4.8; 95% CI, 2.1-11.3) than the female partners of asymptomatic men. Pelvic inflammatory disease was not more likely to be diagnosed in the female partners ofmen with genitalwarts (AOR, 1.4; 95% CI, 0.5-4.4) or candidiasis (AOR, 1.2; 95% CI, 0.4-3.5) than the female partners of asymptomatic men. The female partners of men with chlamydia experienced post coital bleeding more (AOR, 1.9; 95% CI, 1.0-3.6) and were more likely to be diagnosed with PID (AOR, 3.6; 95% CI, 1.6-8.0). Conclusions: The female partners of men with pathogen-negative NGU may be at increased risk of genital infection, even if a recognised pathogen is not identified in the man.