The objective of this study was to estimate local at-risk populations of men who have sex with men (MSM) in London primary care trusts (PCTs) to inform the commissioning of targeted health interventions. Estimated population size and prevalence of diagnosed HIV in MSM in all of London were calculated using data from the British National Survey of Sexual Attitudes and Lifestyles (NATSAL), Greater London Authority population estimates and the annual survey of diagnosed MSM (Survey of Prevalent HIV Infections Diagnosed [SOPHID]). Estimated MSM population sizes at the PCT level were calculated using un-weighted and SOPHID-weighted methods and methods discussed. Four-fifths of MSM with diagnosed HIV infection in Greater London lived in inner London. Estimated population size of MSM 16-44 years in inner London was 66,000; estimated overall prevalence of diagnosed HIV infection among MSM was 9.5%. Our models show substantial variation at the PCT level between the two methods. Using the SOPHID-weighted method MSM account for up to 16% of the male population in some London PCTs, compared with as low as 3% in others. We provide a novel method of estimating at-risk MSM populations living in inner London PCTs indicating that proportions of MSM vary widely between PCTs. Significant proportions of MSM among the resident populations in several PCTs warrant inclusion of MSM health needs in core PCT prevention and service programming. In light of data source limitations further validation studies are needed.