Background: The collection of routine clinical data in the setting of research registries can serve an important role in understanding real world care. However, relatively little is known about the patient experience in registries, motivating us to survey patients enrolled in two chronic disease registries. Methods: We conducted similar surveys in two disease-based registries based at one academic medical center in the US. One group of patients with rheumatoid arthritis (RA) had been enrolled in a registry, and we focused on retention factors. In a second group of patients with inflammatory bowel disease (IBD) recently enrolled or considering enrollment, we examined factors that would influence their enrollment and willingness to answer frequent questionnaires and give biospecimens. The surveys were analyzed using descriptive statistics and the two cohorts were compared using nonparametric and chi-square tests. Results: We received 150 (50%) completed surveys from RA and 169 (63%) from IBD patients. Mean age of subjects was 62 years in RA and 43 in IBD with more women respondents with RA (83%) than IBD (62%). The two groups described very similar factors as the top three motivations for participation: desire to help others, desire to improve care of own disease, and ease of volunteering. Preferred methods of surveying included mail, e-mail, but telephone was not favored; age was an important correlate of this preference. Respondents preferred surveys either every 1-3 months (28.7% RA and 55.0% IBD) or every 4-6 months (50.7% RA and 29.0% IBD). They differed in the preference for payment for answering surveys with 68.0% with RA answering that no payment was necessary but only 36.1% with IBD felt similarly. Conclusions: Patients engaged in clinical registries demonstrate a high level of commitment to improve care and many report a willingness to answer questions relatively frequently.