Objective To identify the optimal measure of active and passive prenatal tobacco exposure to predict wheeze in early life. Study design We conducted a birth cohort study of 398 mother-infant dyads enrolled during the second trimester of pregnancy and followed through age 2 years. We measured tobacco exposure with maternal report, serum cotinine level, and meconium cotinine level. We assessed wheeze with parent report every 6 months. We used a repeated measures logistic regression model. Results Of 367 children with respiratory data, 26% percent had parent reported active or passive prenatal maternal tobacco exposure, but cotinine was detected in 61% of mothers during pregnancy. Compared with children of mothers in the fifth percentile of tobacco exposure, children of mothers in the 95th percentile had increased odds of wheeze when exposure was measured with maternal serum cotinine level (adjusted OR, 2.6; 95% CI, 1.3-5.2; P  < .006) versus meconium cotinine level (adjusted OR, 2.0; 95% CI, 1.0-4.0; P = .04) and total parent-reported exposure (adjusted OR, 1.7; 95% CI, 1.1-2.7; P = .01). Conclusions Serum cotinine, a biomarker of tobacco exposure, was more strongly associated with wheeze than parent-reported exposure. Studies that rely on parent report of prenatal tobacco exposure may underestimate risk of wheeze.