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Abstract Background Self-administered questionnaires are becoming increasingly common in general practice. Much research has explored methods to increase response rates but comparatively few studies have explored the effect of questionnaire administration on reported answers. Methods The aim of this study was to determine the effect on responses of returning patient questionnaires to the respondents' medical practice or an independent researcher to questions relating to adherence and satisfaction with a GP consultation. One medical practice in Waveney primary care trust, Suffolk, England participated in this randomised trial. Patients over 18 years initiated on a new long-term medication during a consultation with a GP were randomly allocated to return a survey from their medical practice to either their medical practice or an independent researcher. The main outcome measures were self reported adherence, satisfaction with information about the newly prescribed medicine, the consultation and involvement in discussions. Results 274 (47%) patients responded to the questionnaire (45% medical practice, 48% independent researcher (95% CI -5 to 11%, p = 0.46)) and the groups appeared demographically comparable, although the high level of non-response limits the ability to assess this. There were no significant differences between the groups with respect to total adherence or any of the satisfaction scales. Five (4%) patients reported altering doses of medication in the medical practice group compared with 18 (13%) in the researcher group (P = 0.009, Fisher's exact test). More patients in the medical practice group reported difficulties using their medication compared to the researcher group (46 (35%) v 30 (21%); p = 0.015, Fisher's exact test). Conclusion Postal satisfaction questionnaires do not appear to be affected by whether they are returned to the patient's own medical practice or an independent researcher. However, returning postal questionnaires relating to detailed patient behaviours may be subject to response biases and further work is needed to explore this phenomena.