Internet access has caused a global revolution in the way people of all ages and genders interact. Many have turned to the Internet to seek love, companionship, and sex, prompting researchers to move behavioral studies online. The sexual behavior of men who have sex with men (MSM) has been more closely studied than that of any other group online given the abundance of gay-oriented websites and concerns about increasing transmission of HIV and other sexually transmitted infections. Not only does the Internet provide a new medium for the conduct of behavioral research and for participant recruitment into an array of research studies, it has the as yet unrealized potential to reach huge numbers of MSM with innovative harm reduction and prevention messages tailored to individualized needs, interests, and risk behavior. Internet-based research on sexual behavior has many advantages in rapidity of recruitment of diverse samples which include individuals unreachable through conventional methods (i.e., non-gay identified and geographically and socially isolated MSM, etc.). Internet-based research also presents some new methodologic challenges in study design, participant recruitment, survey implementation, and interpretation of results. In addition, there are ethical issues unique to online research including difficulties in verifying informed consent, obstacles to surveying minors, and the ability to assure anonymity. This paper presents a review of Internet-based research on sexual behavior in MSM, a general discussion of the methodologic and ethical challenges of Internet-based research, and recommendations for future interdisciplinary research.