We conducted a qualitative study to examine users' perceptions of a web-based screening and referral system for young adults with health-related social problems. The first 50 patients who used the system also took part in semi-structured interviews. There were 20 patients aged 15-17 years and 30 aged 18-25 years. Completing the web-based screening process took an average of 25 min. Ninety percent of participants reported at least one major health-related social problem and a total of 134 referrals were selected for further assistance. Ninety-six percent of participants said they would recommend the system to a friend or peer, and 80% supported its use for annual screening. Perceived strengths of the system were novelty, privacy, ease of use, relevance, motivation, variety and proximity of referrals, and clinic staff support. Perceived shortcomings were length, sensitivity, navigation challenges and agency availability. The system complemented provider visits and preserved privacy while improving attention to patient needs. Computerized screening and referral tools have potential to improve the quality of care in vulnerable young adults.