The purpose of this study was to determine the efficacy and cost-effectiveness of an intensive smoking cessation intervention that utilizes extended cognitive-behavioral therapy and combination nicotine replacement (CNR) in a randomized controlled trial. The intensive intervention was compared to usual care involving referral to a free-standing smoking cessation program that provides brief counseling and CNR. We recruited 162 smokers, ages 18 to 75, who are enrolled in the Drug and Alcohol Treatment (DAT) programs at the San Francisco VA Medical Center (SFVAMC) and Santa Rosa VA Community-based Outpatient Clinic (CBOC). To be eligible, participants had to be abstinent from alcohol for at least one week, but not more than 30 days. We compared outcomes for the two study arms by assessing biochemically-validated point-prevalence smoking status at 3, 6, 9, and 12 months post-baseline and continuous abstinence over the 12-month follow-up. Expired-air carbon monoxide (CO) was used to biochemically verify 7-day point prevalence abstinence. We also conducted an economic analysis to determine the cost-effectiveness of the intensive intervention compared with usual care. We also examined cross-relapse patterns during the follow-up period, assessing changes in mood states and use of tobacco, alcohol, and other drugs at 3, 6, 9, and 12 months.