Background: Chest pain is a common complaint and reason for consultation in primary care. Few data exist from a primary care setting whether male patients are treated differently than female patients. We examined whether there are gender differences in general physiciansxxx (GPs) initial assessment and subsequent management of patients with chest pain, and how these differences can be explained Methods: We conducted a prospective study with 1212 consecutive chest pain patients. The study was conducted in 74 primary care offices in Germany from October 2005 to July 2006. After a follow up period of 6 months, an independent interdisciplinary reference panel reviewed clinical data of every patient and decided about the etiology of chest pain at the time of patient recruitment (delayed type-reference standard). We adjusted gender differences of six process indicators for different models. Results: GPs tended to assume that CHD is the cause of chest pain more often in male patients and referred more men for an exercise test (women 4.1%, men 7.3%, p = 0.02) and to the hospital (women 2.9%, men 6.6%, p < 0.01). These differences remained when adjusting for age and cardiac risk factors but ceased to exist after adjusting for the typicality of chest pain. Conclusions: While observed gender differences can not be explained by differences in age, CHD prevalence, and underlying risk factors, the less typical symptom presentation in women might be an underlying factor. However this does not seem to result in suboptimal management in women but rather in overuse of services for men. We consider our conclusions rather hypothesis generating and larger studies will be necessary to prove our proposed model.