Using two cohort studies (Health in men-HIM and positive health-PH) and repeated large cross-sectional surveys (Gay Community Periodic Survey-GCPS) of gay men in Sydney, Australia, we examined the association between viral load and unprotected anal intercourse (UAI) between HIV sero-discordant regular partners. Between 2001 and 2007, we conducted 243 interviews with 102 HIV-negative gay men in HIM and 148 interviews with 99 HIV-positive gay men in PH who were in regular relationships with HIV sero-discordant partners. During the same time period, 437 HIV positive men with HIV sero-discordant regular partners completed questionnaires for the GCPS. All completed interviews or questionnaires during that time period were used for these analyses. Amongst the HIV-negative respondents, sero-discordant UAI was more likely to be reported when the men believed their HIV-positive regular partner had an undetectable rather than a detectable viral load (P = 0.002). Amongst the HIV-positive respondents, sero-discordant UAI was as likely to be reported when they themselves reported having an undetectable or a detectable viral load. Use of viral load in negotiating condom use between sero-discordant gay couples may be understood very differently by the HIV-negative and HIV-positive men within those partnerships.