OBJECTIVES: Bipolar disorder (BPD) is a debilitating recurrent chronic mental illness, characterized by cycling states of depression, mania, hypomania, and mixed episodes.  The objectives of this study were to calculate national estimates of the annual burden of inpatient hospitalizations of children and adolescents with bipolar disorder (BPD); to describe and compare the burden across various patient characteristics, hospital characteristics, and key comorbidities associated with BPD; and to determine the independent effects of these factors on hospitalization costs. METHODS: Discharge observations for children whose primary diagnosis was BPD were collected from the Kids' Inpatient Database (KID). The burden was estimated as total number of days in the hospital, total charges, and total costs.  Mean costs and charges were calculated and were broken down by patient and hospital characteristics and by the top six comorbidities found for BPD.  Ordinary–least-squares regression models explaining cost were estimated for both 2003 and 2006, and the models were compared by way of a Chow test. RESULTS: There were 39,136 (40,679) bipolar disorder discharges in 2003 (2006), with total associated costs of $176 ($233) million in 2003 (2006).  The mean cost was $4,490 ($5,725), while the mean length of stay was 8.12 (8.99) days in 2003 (2006).  Factors associated with higher cost included youth (younger than 13), being black, being from a high-income family, having many diagnoses, being insured by Medicaid, living in the North East or West regions of the country, and having a long hospital stay. CONCLUSIONS: Declining trends in mean cost and length of stay, documented in previous studies for children with BPD, persisted into 2003 but showed a slight reversal by 2006.