BACKGROUND: The management of patients in primary care is often complicated by the presence of multiple chronic conditions and psychosocial issues that increase the complexity of the encounter and have important impacts on care. There is a paucity of literature on this subject in the pediatric population. OBJECTIVES: The aim of this study was to quantify the burden of chronic conditions in pediatric primary care. METHODS: The problem lists of 3995 randomly selected patients from a community pediatric clinic and an academic hospital-based pediatric clinic in the same metropolitan area were analyzed for the presence and number of any chronic condition. RESULTS: In total, 53% of patients suffered from at least one chronic problem, 25% had two or more chronic conditions and 5.1% had four or more conditions. Compared with the community clinic, the academic clinic had significantly more children with catastrophic complex conditions (P<0.001). A regression analysis showed a significant positive correlation between the number of chronic medical conditions and mental health diagnoses. CONCLUSIONS: The burden of chronic disease in the pediatric primary care setting may be significantly higher than has been previously suggested. To ensure optimal quality of care, health planners should take into account the high burden of chronic illness, psychosocial issues and multimorbidity among patients in the pediatric primary care setting, as well as the higher complexity profile of patients attending academic clinics.