The significance of asymptomatic non-chlamydial non-gonococcal urethritis (NCNGU) is unclear. Organisms associated with NCNGU, e.g. Mycoplasma genitalium, for which there is no widely available test, are linked to reproductive sequelae in women but UK guidance no longer recommends urethral smear microscopy to screen for asymptomatic NCNGU. This case-control study of heterosexual male genitourinary (GU) medicine clinic attenders aimed to identify clinical, demographic and sexual behaviour factors associated with asymptomatic NCNGU so that we could determine whether the presence or absence of symptoms provides a rational basis for deciding to whom we should offer microscopy and whom we should treat. Men with asymptomatic NCNGU were very similar to men with symptomatic NCNGU, except for more consistent condom use. Asymptomatic and symptomatic NCNGU could be different ends of the same clinical syndrome. Until the microbiological basis of NCNGU is understood, we recommend treatment of men with NCNGU irrespective of symptoms.