The prevalence of pain complaints as a reason for patient-doctor encounters in the local primary care setting is unknown. We performed a cross-sectional survey of such encounters in one public primary care clinic (KK) and 17 general practice clinics (GP), from the city of Seremban, Negeri Sembilan, Malaysia. Reasons for visits were recorded by doctors in KK and medical students in GP using a structured questionnaire. Morbidity data was coded using the International Classification of Primary Care (ICPC-2). A total of 2234 encounters were recorded (80.9% from KK, 19.1% from GP). The overall prevalence of pain complaints was 31.9% with a significant difference between the two cohorts (KK 28.7% and GP 45.2%, p<0.001). Musculoskeletal pain complaints were more common in KK than GP (40.9% versus 29.7%, p<0.05). Of the 3 main ethnic groups in Malaysia (Malay, Chinese and Indian) the Indian patients at KK had the highest prevalence of pain complaints and the Chinese at the GP had the lowest. Thus pain was a common complaint in the two different primary care settings studied. Some of the differences observed are probably due to the differences in the healthcare seeking behaviour of patients consulting at these two settings as well as differences in the payment systems.