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The relationship between erectile dysfunction drugs and the immune system is unclear. There have been animal studies in the past to support a biological rationale for these drugs to have immunomodulatory effects on the levels of immune markers. This study examines the effect of erectile dysfunction drugs in both HIV positive and negative men who have sex with men. Over one thousand men with semi-annual visits from the Multicenter AIDS Cohort Study provided data ranging from demographics to sensitive information on sexual activities, CD4/8 T-cells and inflammatory biomarkers. Study participants with age ranging from 19 to 70 were only included from 1998 onward, which was when the erectile dysfunction drugs were available. Bivariate random-intercept models were used to assess correlations between erectile dysfunction drug use and other behavioral factors over time at both population and individual levels. Recreational drugs use and engagement in risky sexual activities, such as unprotected anal intercourse, were positively associated with erectile dysfunction drug use. By applying marginal structural models for causal inference in a complex longitudinal setting, we provided evidence to show improved immune capacity, exhibited by increased CD4 cell counts and percentages, in HIV positive men who reported both short and long-term drug use. We showed further evidence of anti-inflammatory effects of using erectile dysfunction drugs and reduced levels of pro-inflammatory markers in both HIV positive and negative men. We conclude that erectile dysfunction drug use demonstrated favorable immunomodulatory effects in men with and without HIV infection.