Rural men who have sex with men (MSM) are heavily affected by HIV, and many lack culturally competent HIV prevention resources. Rural MSM may find sexual partners on the internet, which may also be a way to deliver prevention services to them. To understand the differences between rural and urban MSM with respect to HIV risk factors and behaviors and the utilization of online HIV prevention services, we used data from the 2012 Web-Based HIV Behavioral Survey (WHBS). Using WHBS data collected between June and August 2012, we compared the characteristics of MSM with positive or unknown HIV infection status who had sex with a male in the past 12 months, from rural vs urban areas using Chi square tests and median tests. We used logistic regression and calculated adjusted prevalence ratios (aPR) and 95% confidence intervals (CI) to compare self-reported HIV risk behaviors, HIV/STI testing behaviors, use of prevention services, and perceived discrimination. Of the 8166 MSM included in our analysis, 3583 (44%) were from rural areas, and 4583 (56%) were from urban areas. Compared to urban MSM, rural MSM were less likely to ever test for HIV (aPR = 0.94, CI 0.92-0.95), to be tested for HIV in the last year (aPR = 0.83, CI 0.79-0.87), or to receive free condoms (aPR = 0.83, CI 0.79-0.86) or individual prevention counseling in the past year (aPR = 0.86, CI 0.78-0.95). Rural MSM were less likely to have been tested in the last year for syphilis, gonorrhea, or chlamydia (aPR = 0.70, CI 0.62-0.78; aPR = 0.72, CI 0.64-0.81; aPR = 0.75, CI 0.67-0.85, respectively). Rural MSM also reported perceiving less tolerance of gays and bisexuals within their community (aPR = 0.80, CI 0.77-0.84). HIV prevalence is lower among MSM in rural areas compared to MSM in urban areas, but rural MSM report that they are more likely to face intolerance and are less likely to use basic HIV prevention services compared to urban MSM. Therefore, this hard-to-reach population could benefit from prevention services offered through the internet.