This audit aimed to determine the usefulness of microscopy to detect presumptive rectal gonorrhoea (GC) infection in asymptomatic men. We retrospectively audited more than 400 male patients attending a London genitourinary medicine clinic from January 2005 to March 2007 who tested rectal culture positive for Neisseria gonorrhoeae and compared this with the microscopy detection rate. In total, 123/423 (29%) of culture positive samples were microscopy positive. Of those that tested microscopy negative (300/423), 64 (21%) were symptomatic and 236 (79%) asymptomatic. In addition, a time and motion study examined 81 rectal slides over a two-week period to identify microscopy reading time required to make a presumptive diagnosis of GC. Three slides were positive, resulting in six hours and 45 minutes to detect one positive sample. Given the low sensitivity for rectal microscopy coupled with the length of time required to obtain a presumptive positive rectal GC result, we believe rectal microscopy is no longer a cost-effective tool screening for asymptomatic men, and this report supports the BASHH guideline that it is not recommended in the management of asymptomatic rectal infection.