Background Behavioral treatments can augment the success of pharmacotherapy in smoking cessation. The aim of this study was to compare smoking quit rates between patients receiving individual counseling with their general practitioner during office visits or intensive counselling with behavioral support, both augmented by varenicline. Methods A nationwide retrospective cohort study conducted in a large Healthcare Maintenance Organization in Israel. We selected randomly patients who filled a prescription for varenicline and received either individual consulting by their general practitioner or intensive counselling with behavioural support, and asked them to answer a questionnaire. The outcome variables were smoking cessation 26–52 weeks following the beginning of treatment and satisfaction with the process. Results 870 patients were contacted and 604 agreed to participate (a response rate of 69%); 301 patients in the general practitioner group, 300 in the intensive counselling group and 3 were excluded due to missing date. The quit rate was 36.5% in the general practitioner group and 42.3% in the intensive counselling group (P = 0.147). In a logistic regression analysis, controlling for age, gender, socioeconomic status, ischemic heart disease, chronic obstructive pulmonary disease, pack years and duration of varenicline consumption, the adjusted OR for quitting in the general practitioner group was 0.79 (95% CI 0.56,1.13). The adjusted OR was higher in the group with the highest socioeconomic status at 2.06 (1.39,3.07) and a longer period of varenicline consumption at 1.30 (1.15,1.47). Age, gender and cigarette pack-years were not associated with quit rate. In the general practitioner group 68% were satisfied with the process, while 19% were not. In the intensive counselling group 64% were satisfied and 14% were not (P = 0.007). Conclusion We did not detect a statistically significant difference in smoking quit rates, though there was a trend towards higher quit rates with intensive counselling.