Background: Studies about beverage preferences in a country in which wine drinking is relatively widespread (like Switzerland) are scarce. Therefore, the main aims of the present study were to examine the associations between beverage preferences and drinking patterns, alcohol-related consequences and the use of other substances among Swiss young men. Methods: The analytical sample consisted of 5399 Swiss men who participated in the Cohort Study on Substance Use Risk Factors (C-SURF) and had been drinking alcohol over the preceding 12 months. Logistic regression analyses were conducted to study the associations between preference for a particular beverage and (i) drinking patterns, (ii) negative alcohol-related consequences and (iii) the (at-risk) use of cigarettes, cannabis and other illicit drugs. Results: Preference for beer was associated with risky drinking patterns and, comparable with a preference for strong alcohol, with the use of illicit substances (cannabis and other illicit drugs). In contrast, a preference for wine was associated with low-risk alcohol consumption and a reduced likelihood of experiencing at least four negative alcohol-related consequences or of daily cigarette smoking. Furthermore, the likelihood of negative outcomes (alcohol-related consequences; use of other substances) increased among people with risky drinking behaviours, independent of beverage preference. Conclusions: In our survey, beer preference was associated with risky drinking patterns and illicit drug use. Alcohol polices to prevent large quantities of alcohol consumption, especially of cheaper spirits like beer, should be considered to reduce total alcohol consumption and the negative consequences associated with these beverage types.