In the United States (US) in 2013, men who have sex with men (MSM) accounted for 75% of reported primary and secondary syphilis and over 80% of new HIV diagnoses. However, describing trends in MSM disparities are challenging. Few estimates of the size of the population of men who have sex with men (MSM) in the US exist. The National Survey of Family Growth (NSFG) is a probability sample of American men and women aged 15–44. We used the weighted proportion of males surveyed during the 2006–2010 cycle of NSFG who reported having ever had sex with men to estimate the population prevalence of MSM in the US; racial/ethnic and age specific were also developed. We estimated the population of MSM by applying the proportions of men who reported ever having sex with a man from NSFG to the 2010 census estimates of the number of men 15–44. Rates of primary and secondary (P&S) syphilis among MSM were calculated by dividing the number of reported P&S syphilis cases among MSM by the estimated US MSM population. Age and racial/ethnic rates were also estimated. Among the 10,403 males participating in the 2006–2010 NSFG cycle, the proportion who reported ever having sex with a man was 5.1%; we estimated 3.2 million MSM aged 15–44 in the US. By applying metrics from a national probability sample of males, we were able to estimate conservative rates of P&S syphilis among important sub-populations of MSM. However, numerous challenges exist to developing robust MSM population-based estimates of disease burden including how to determine the gender of sex partners on male case reports for syphilis, chlamydia, gonorrhoea, and HIV and the estimation of sub-population specific denominators (e.g. racial/ethnic groups) for MSM.