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Objective To inform providers and policy-makers about the potential costs of providing physical health care in mental health clinics. Methods Cost data were collected through interviews with 22 behavioral health clinics participating in New York State Office of Mental Health's health monitoring and health physicals programs. The interview data was combined with financial reporting data provided to the state to identify per interaction costs for two levels of physical health services: health monitoring and health monitoring plus health physicals. Results This study gives detailed information on the costs of clinics' health integration programs, including per interaction costs related to direct service, charting and administration, and total care coordination. Average direct costs per client interaction were 3 times higher for health physicals than for health monitoring. Conclusions Costs of integrating physical care services are not trivial to mental health clinics, and may pose a barrier to widespread adoption. Provision of limited health monitoring services is less expensive for clinics, but generates proportionally large non-clinical costs than health physicals. The relative health impact of this more limited approach is an important area for future study. Also, shifting reimbursement to include health care coordination time may improve program sustainability.