New forms of HIV pre-exposure prophylaxis (PrEP) include long-acting injectables and topical microbicides, each with unique attributes that may appeal to distinct users. We used a discrete choice experiment to characterize preferences for new PrEP formulations among Toronto men who have sex with men. MSM undergoing anonymous HIV testing completed a discrete choice experiment with 12 choice sets by selecting their preferred option within each set. Each set included “usual methods to prevent HIV” (excluding PrEP) as one alternative and two hypothetical PrEP alternatives, which differed according formulation/dosing, side effects (none/mild), risk of drug resistance (none/low/moderate), and HIV prevention efficacy (50%, 65%, 80% or 99% risk reduction). We used mixed logistic regression to infer preferences for PrEP attributes and calculate the marginal rate of substitution between efficacy and other PrEP attributes. 306 men with median (interquartile range) age = 29 (25, 36) years participated, and reported 6 (3, 10) partners and 0 (0, 2) condomless receptive anal sex acts in the preceding six months. An on-demand pill was the most preferred formulation, followed by a monthly injection, daily pill, and on-demand rectal gel. Drug resistance was an important determinant of preferences if the risk was moderate, but not if it was low. The minimum efficacy required for an on-demand pill to be preferred over no PrEP was 32.6% (95%CI = 21.2–43.9%); for a daily pill, injections, and rectal gel, minimum efficacy was 57.9% (95%CI = 44.1–71.7%), 40.1% (27.0–53.2%), and 71.3% (60.5–82.1%), respectively. Attitudes towards PrEP formulations vary among men who have sex with men, with on-demand pills and monthly injections having the highest average preference scores. Understanding these preferences may help to predict uptake.