The clinical pharmacology of biochemical measures of nicotine exposure has been thoroughly reviewed with regard to usefulness and limitations in detecting abstinence from cigarette smoking. While plasma nicotine concentration measures only acute nicotine exposure, plasma, salivary, and urine cotinine concentrations reflect exposure over an extended period of time. Although, expired carbon monoxide (CO) is frequently used to confirm self reports, it has a relatively short half life, calling into question whether this measure might provide misleading information by exaggerating smoking cessation success rates. To examine this question, we analyzed expired CO, plasma cotinine and self report data collected in a clinical trial in which subjects (N=207) were randomly assigned to gain- or loss-framed messages for smoking cessation in combination with open label sustained-release bupropion (300 mg/day). In examining measurements collected at 6 weeks, 3 and 6 months, results showed that CO significantly overestimated abstinence rates as compared with cotinine, although the discrepancy was less at the later time points. These data suggest that while expired CO is a useful and well-established marker in certain contexts, when testing extended abstinence from smoking with non-nicotine medications, cotinine measurements should be preferred.