Background: The perception of the risk of sexually transmitted infections (STIs) is a well-researched phenomenon, but not in relation to cyberchondria and health literacy. Therefore, our aim was to examine the association between the assessment of the risk of sexually transmitted diseases and HIV, cyberchondria, and health literacy. Materials and methods: This study was conducted in 2020-2021 in Croatia. The experimental group consisted of patients from the Centre for Voluntary Counselling and Testing for HIV (N = 134). The control group consisted of other patients recruited from daily epidemiological practices (N = 171). The instruments that were used were questionnaires that measure the perception of risk of sexually transmitted infections and HIV, health literacy, and cyberchondria. Results: Out of 305 respondents, 134 (43.9%) were in the STI counselling group, and 171 (56.1%) were in the control group. Generally, the participants in the former perceived the risk of sexually transmitted infections and HIV to be higher (but still low) than those in the latter. There was no difference in health literacy between the STI and control group; the health literacy score was average in both groups. There were differences in almost all the cyberchondria factors, except for Mistrust. Health literacy, belonging to the STI counselling group, and risk behaviours were positively associated with CH in the logistic regression analysis. Conclusions: People with a risk for STIs tend to minimize this risk, have higher cyberchondria levels, and have average health literacy. Cyberchondria is positively associated with health literacy, and more education about excessive health-related internet research is needed.