Background Smoking has been associated with postoperative complications and mortality in bariatric surgery. The evidence for smoking is based on self-report and medical charts, which can lead to misclassification and miscalculation of the associations. Determination of cotinine can objectively define nicotine exposure. We determined the accuracy of self-reported smoking compared to cotinine measurement in three phases of the bariatric surgery trajectory. Methods Patients in the phase of screening (screening), on the day of surgery (surgery), and more than 18 months after surgery (follow-up) were consecutively selected. Self-reported smoking was registered and serum cotinine was measured. We evaluated the accuracy of self-reported smoking compared to cotinine, and the level of agreement between self-report and cotinine for each phase. Results In total, 715 patients were included. In the screening, surgery, and follow-up group, 25.6%, 18.0%, and 15.5%, respectively, was smoking based on cotinine. The sensitivity of self-reported smoking was 72.5%, 31.0%, and 93.5% in the screening, surgery, and follow-up group, respectively (p < 0.001). The specificity of self-report was > 95% in all groups (p < 0.02). The level of agreement between self-report and cotinine was 0.778, 0.414, and 0.855 for the screening, surgery, and follow-up group, respectively. Conclusions Underreporting of smoking occurs before bariatric surgery, mainly on the day of surgery. Future studies on effects of smoking and smoking cessation in bariatric surgery should include methods taking into account the issue of underreporting.