Introduction: Men who have sex with men (MSM) in Kenya face a disproportionate HIV disease burden. Over the last few years, the use of virtual platforms and internet sites to seek male sexual partners has increased manyfold in Kenya. New approaches are required to map, estimate and profile MSM who operate through virtual platforms to design interventions for them. Methods: This study was conducted in three counties in Kenya: Kiambu, Kisumu and Mombasa with MSM who use virtual platforms such as geosocial networking (GSN) and social networking applications to find and connect with male sex partners. The platforms were profiled through a multi-stage approach and the number of MSM associated with these platforms were estimated. In the final stage, 435 respondents randomly selected from the virtual platforms were interviewed in a secure location after informed consent. Data analysis focused on calculating an estimate of MSM for each virtual platform in each site, adjusting for duplicate profiles and multiple registrations. Results: We identified 24 GSN apps, 18 Facebook accounts/pages and 18 WhatsApp groups across the three counties, with Facebook being the preferred platform. Kiambu had the highest number of estimated MSM at 3,635 (95%CI = 3,335 to 3,990) followed by Kisumu at 1,567 (95%CI = 1,480 to 1,665) and Mombasa at 1,469 (95%CI = 1,335 to 1,604) who used virtual platforms to find other male sexual partners. On average, each MSM had 3.7 profiles on multiple platforms, with an average of 2.1 profiles used in the past month. Conclusions: The use of conventional population size estimation approaches that focus on physical sites alone may underestimate the total number of MSM in a geography. Virtual mapping should be used in conjunction with conventional hot spot based size estimation methodologies to estimate numbers of MSM to set programmatic targets.