Tobacco use is a risk factor for adverse outcomes among hematopoietic SCT (HSCT) patients. Accurate identification of tobacco use offers a vital opportunity to treat this risk factor. The current study compared self-reported tobacco use status with serum cotinine levels among HSCT patients at the time of pre-transplant evaluation. A total of 444 participants completed both assessments; 44 participants (9.9%) were classified as tobacco users with serum cotinine concentrations >2 ng/mL vs 29 with self-reporting. Sensitivity and specificity of self-reporting were 65.9% and 100%, respectively. Positive and negative predictive values were 100% and 96.4%, respectively. Comparing tobacco use documented in the medical record with cotinine, sensitivity and specificity were 51.2% and 99.2%, respectively. Factors associated with tobacco use were male gender, single relationship status, less education and younger age. In summary, utilization of serum cotinine assays increased detection of tobacco use cases >50% over self-reporting. Results are discussed in the context of translation to care, including clinical and ethical implications, and current tobacco use treatment guidelines. When cotinine assays are not available, self-reporting of any tobacco use in the year before HSCT should trigger brief advice and cessation or relapse prevention counseling.