National data that examine health costs among children with special needs are limited and do not address children with orofacial clefts (OFC). This study examines Medicaid expenditures among children with and without OFC. North Carolina vital statistics, health services, birth defects registry, and Medicaid enrollment and paid claims were linked to identify resident children born 1995-2002 with and without OFC who were continuously enrolled in Medicaid. Outcome measures included average cost per child for medical, inpatient, outpatient, dental, well-child care, mental health, and home health. Average expenditures per child were also determined and were examined by the child's phenotypic characteristics including type of cleft and whether the defect was isolated or non-isolated. Expenditure ratios were calculated to compare cases and controls and differences in expenditures among cases by cleft type and by isolated/non-isolated occurrence. During infancy, average mental health expenditure per child with OFC was 37.2 times higher than for a child without OFC. Average home health expenditure per case was 45.0 times higher than for a control. Mean expenditure per child with OFC was $22,642 compared to $3,900 for an unaffected child. Mean expenditure for a child with cleft palate and child with cleft lip with cleft palate were about three times more than a child with cleft lip alone. Mean expenditure per child with non-isolated OFC also was substantially higher than the expenditure for a child with isolated OFC. Children with OFC have significantly higher health-related Medicaid expenditures than unaffected children. These findings are important for targeting care coordination and early intervention and for program planning and policy development related to special needs children.