The aim of this study was to ascertain how sexual health physicians in Australia and New Zealand manage men with chlamydia-negative non-gonococcal urethritis (NGU), particularly in relation to the notification of their female sexual partners. In July 2006, a cross-section survey was sent out to all the members of the Australasian Chapter of Sexual Health Medicine. Seventy-three percent of sexual health physicians believed that female partners of men who present with chlamydia-negative NGU were at risk of adverse reproductive health outcomes. At least 62% usually initiated some form of partner notification of female partners of men with chlamydia-negative NGU. However, only 19% (21/111) of sexual health physicians routinely tested for, and only 65% sometimes tested for, pathogens other than Neisseria gonorrhoeae and Chlamydia trachomatis in men presenting with NGU. These included Mycoplasma genitalium, herpes simplex virus, ureaplasma species, Trichomonas vaginalis and adenoviruses.