When communicating about health behaviour with students, insight is needed in perceptions students have about their (un)healthy behaviour. We aimed to investigate associations between problem perception and perceived health, academic functioning in students using tobacco, alcohol or drugs. Students who were enrolled fulltime in Medicine, Economics, Occupational Therapy, History, Psychology or Information Studies in Amsterdam, the Netherlands (n = 8258), were invited for an internet-based questionnaire about perceived health, social support, study delay, and problem perception regarding tobacco, alcohol and drug use in October 2005 (response: 44%). Students using tobacco, alcohol and drugs with and without problem perception and non-users were compared (logistic regression). Problem perception in students using tobacco, alcohol or drugs was associated with worse health outcomes.