HPV vaccines are available to men but there are few studies investigating the acceptability of HPV vaccines among men who have sex with men (MSM), a high risk group. We assessed the intention to take up HPV vaccines among MSM in Hong Kong and the associated factors related to cognitions on HPV and HPV vaccines, basing on the Health Belief Model (n = 542). The acceptability of HPV vaccines was 20% (unconditional on efficacies and price), 29.2% (conditional on efficacies and market price), 51.7% (conditional on efficacies and discounted price) and 79.1% (conditional on efficacies and free price). Adjusting for background variables, composite scores of perceived susceptibility, perceived severity, perceived barriers and cue to actions were significantly associated with acceptability of HPV vaccines conditional on specific efficacies and the market price. Acceptability of HPV vaccines was highly price sensitive. Future studies need to use conditional measures. Implementation and translational researches are warranted.