The primary care physician can play an important role in helping patients with congenital anomalies and their families begin to approach the complex medical, psychosocial, and philosophical questions that commonly arise. Identification of a specific genetic etiology or category of disease can be made by employing a systematic approach to determine the likely pathogenesis of the birth defects and fitting this understanding into a clinical pattern of how distinct anomalies interrelate. The primary physician can initiate diagnostic genetic testing for suspected malformation syndromes and sequences before referral to a medical genetics specialist for further evaluation and counseling. Optimal management of patients with severe anomalies or complicated medical problems requires a multidisciplinary approach that is guided by an accurate diagnosis. The primary care physician is in the best position to coordinate this effort to provide the most beneficial interventions to maximize the potential of a child with congenital anomalies.