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Background: For evidence-based decision making in family practice, it is essential to know the long-term (natural) course of common diseases and their outcomes under care and treatment. This article, based on a research methodology workshop, aims to raise awareness and interest in longitudinal research in practice-based research networks (PBRNs) among family physicians (FP) and researchers, and to elucidate a number of broad principles that apply to longitudinal research in such settings., Methods: A workshop discussion of PBRN experts, based on 2 examples of PBRN-based longitudinal studies, focusing on the general methodological principles was held in March 2005 in Colorado Springs, CO. The first study, conducted in a historic cohort, documented long-term outcome of depression in 386 patients in family practice. The second study analyzed consequences of age-associated peripheral neuropathy in a concurrent follow-up study design. It was possible to prospectively follow a cohort of 604 healthy subjects enrolled in the practices by research nurses. Discussion at the workshop was generated around the following methodological topics: study designs, recruitment, retention and tracking of participants, dealing with changes in diagnostic and treatment of standards over time, informed consent, data analysis, and funding issues., Results and Conclusions: The workshop concluded that, although there are many obstacles to be overcome when conducting longitudinal studies in practice settings, the benefits for our discipline could be substantial. Concurrent and historic cohorts each have advantages and disadvantages. Although tracking patients (and physicians) over time is a challenge, periodic rewards enhance recruitment and retention. Informed consent is critical although ethical requirements may change. Use of standard well-defined definitions promotes consistency of data collection over time, as does training of FPs and staff. Data analysis has become both easier and more sophisticated, and statistical assistance is advised from the outset. Funding remains a challenge, but costs need not be prohibitive. Given its importance, PBRNs should be encouraged to develop methods of long-term data collection on cohorts of patients followed by primary care physicians.