Introduction: Perceived health risk (PHR) of a tobacco product may influence both uptake and continued use. In this study, we examined PHRs of snus and medicinal nicotine using the PHR scale and the relationship of PHR responses to use of these products in smokers seeking an alternative to smoking. Methods: Smokers were randomly assigned to snus or to medicinal nicotine for a period of 12 weeks and asked to only use the assigned product. The PHR scale involves rating the extent of perceived risk of a product for different diseases and was given at baseline and weeks 4 and 12 during treatment. Relationships between PHR scale scores and study attrition, compliance with only using the product, and continued use of the product after treatment were determined. Results: Response to the PHR scale showed no significant differences between the snus and medicinal nicotine for perceived risks for lung cancer, emphysema, and bronchitis. However, significant differences were observed for other cancers, heart disease, stroke and risk for addiction, particularly after product use, with higher scores among those assigned to snus. Scores on the PHR scale were not related to any of the trial outcome variables. Conclusions: Among smokers seeking an alternative to smoking in a clinic setting, PHR of a product changes after product use but may not be related to product use patterns. Implications: PHRs of snus or medicinal nicotine in smokers assigned to these products become more accurate after product use. PHR does not appear to be associated with patterns of product use; rather satisfaction with a product is a better indicator as to whether a smoker is compliant with only using the product or continues to use the product.