Estimating the size of key affected populations (KAP) provides important data for planning and implementing an effective response to the HIV epidemic. In the Philippines, these KAP include males who have sex with males (MSM), female sex workers (FSW), and injecting drug users (IDU). Given the difficulty in reaching these populations, as well as their high mobility, the process consequently entailed a specific methodology to directly estimate the size of KAP.<br> The national estimate of MSM was 531,500 or 2.2% (1.8%-3.2%) of males aged 15-49. Within this MSM estimate, figures for transgender women (TGW) and male transactional sex workers (MSW) were determined. The national estimate for TGW was 122,800 or about 0.50% (0.40%-0.75%) of males aged 15-49, and 23% of the MSM population. Meanwhile, MSW comprised 0.35% (0.29%-0.53%) of the male population aged 15-49 and 16% of the MSM population, giving a best estimate of 86,600.<br> The estimate of combined RFSW and FFSW was 66,100 or 0.28% (0.19%-0.40%) of females aged 15-49. Meanwhile, there are approximately 10,000 to 21,700 IDU or 0.04%-0.09% of males aged 15-49.