Primary care consultation data are an important source of information on morbidity prevalence. It is not known how reliable such figures are. To compare annual consultation prevalence estimates for musculoskeletal conditions derived from four general practice consultation databases. Retrospective study of general practice consultation records. Three national general practice consultation databases: i) Fourth Morbidity Statistics from General Practice (MSGP4, 1991/92), ii) Royal College of General Practitioners Weekly Returns Service (RCGP WRS, 2001), and iii) General Practice Research Database (GPRD, 1991 and 2001); and one regional database (Consultations in Primary Care Archive, 2001). Age-sex standardized persons consulting annual prevalence rates for musculoskeletal conditions overall, rheumatoid arthritis, osteoarthritis and arthralgia were derived for patients aged 15 years and over. GPRD prevalence of any musculoskeletal condition, rheumatoid arthritis and osteoarthritis was lower than that of the other databases. This is likely to be due to GPs not needing to record every consultation made for a chronic condition. MSGP4 gave the highest prevalence for osteoarthritis but low prevalence of arthralgia which reflects encouragement for GPs to use diagnostic rather than symptom codes. Considerable variation exists in consultation prevalence estimates for musculoskeletal conditions. Researchers and health service planners should be aware that estimates of disease occurrence based on consultation will be influenced by choice of database. This is likely to be true for other chronic diseases and where alternative symptom labels exist for a disease. RCGP WRS may give the most reliable prevalence figures for musculoskeletal and other chronic diseases.