To describe a Web-based computer health assessment survey for patients with rheumatoid arthritis (RA) and to evaluate the survey in comparison with current paper versions. Utilizing data from a study on RA, we compared results from 43 patients attending a university-based clinic who were each given a paper and a demonstration computer version of a patient self-assessment questionnaire including multiple-choice questions from a multi-dimensional Health Assessment Questionnaire (HAQ); visual analog scales (VAS) for pain, fatigue, and global disease severity; and a tender and swollen joint count reporting tool. Patients were given optional followup surveys to determine their opinion of the computer program. High correlations (intraclass correlation coefficient > 0.9) were seen across methods for the 10-item HAQ and psychological distress scores and the VAS scores for pain and global disease severity. Moderate correlation was observed for the self-efficacy scores, the VAS scores for fatigue, and tender joint counts. The data also revealed a small shift in the mean scores for the HAQ and self-efficacy questions, with patients reporting slightly higher scores on the computer instrument. Overall, patient opinions of the uniquely designed joint count tool were good, with 71% of responding patients answering favorably. Web-based computer versions of patient self-assessment surveys in RA are comparable to paper versions, and their use in clinics or over the Internet could dramatically facilitate the ability of physicians to monitor patients' health.