Background: Post-traumatic stress disorder (PTSD) is associated with a high prevalence of smoking, heavy cigarette consumption and low cessation rates. Purpose: This manuscript describes the design of a randomized, multisite effectiveness trial to test whether integrating smoking cessation treatment into mental health care (integrated care) improves prolonged abstinence rates among veterans with PTSD, compared with referral to specialized smoking cessation clinics (usual standard of care). Secondary objectives are to assess the cost-effectiveness of integrated care relative to usual standard of care, identify treatment variables that mediate differences between conditions in outcome and determine whether smoking cessation is associated with worsening PTSD and/or depression. Methods: Following randomization, subjects (projected n = 1400) from 10 Veterans Health Administration (VHA) medical centers complete follow-up assessments every three or six months for up to four years. Endpoints include 1-year prolonged abstinence at 18 months postrandomization, 7- and 30-day point-prevalence abstinence and measures of depression, PTSD and economic outcomes. Results: This study is unique in providing the largest scale test of the feasibility and effectiveness of having mental health clinicians implement evidence-based smoking cessation treatment in psychiatric care settings for veterans with PTSD. It incorporates methodological features that are desirable for cessation treatment trials, including: a) assessment of clinically meaningful long-term smoking outcomes; b) a manual guiding delivery of the experimental intervention; c) independent ratings of clinician competence and treatment adherence and d) methods for training clinicians that would enhance implementation of tobacco cessation treatment in large health care systems. Limitations: Use of an exclusively VHA sample with few females limits generalizability. Conclusions: The process for meeting challenges in designing this study may provide planning of other large-scale clinical effectiveness trials in tobacco control. Findings have potential to initiate system-wide change in clinical practice patterns for tobacco cessation treatment involving patients with mental disorders.