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This study assesses the current practices of Federally Qualified Health Centers (FQHCs) to address tobacco cessation with patients. A national sample of 112 FQHC medical directors completed the web-based survey. Frequently endorsed barriers to providing tobacco cessation services were: patients lacking insurance coverage (35%), limited transportation (27%), and variance in coverage of cessation services by insurance type (26%). Nearly 50% indicated that two or more tobacco cessation resources met the needs of their patients; 25% had one resource, and the remaining 25% had no resources. There were no differences among resource groups in the use of electronic health record (EHR) best-practice-alerts for tobacco use or in the perceived barriers to providing tobacco cessation assistance. Systems changes to harmonize coverage of tobacco assistance, such as broader accessibility to evidence-based cessation services could have a positive impact on the efforts of FQHCs to provide tobacco cessation assistance to their patients.