Objective To examine the dose-dependent and time-specific relationships of prenatal smoking with neonatal body mass, fat mass (FM), fat-free mass (FFM), and FM-to-FFM ratio, as measured by air-displacement plethysmography (PEA POD system). Study design We analyzed 916 mother–neonate pairs participating in the longitudinal prebirth cohort Healthy Start study. Maternal prenatal smoking information was collected in early, middle, and late pregnancy by self-report. Neonatal body composition was measured with the PEA POD system after delivery. Multiple general linear regression models were adjusted for maternal and neonatal characteristics. Results Each additional pack of cigarettes smoked during pregnancy was associated with significant decreases in neonatal body mass (adjusted mean difference, −2.8 g; 95% CI, −3.9 to −1.8 g; P < .001), FM (−0.7 g; 95% CI, −1.1 to −0.3 g; P < .001), and FFM (−2.1 g; 95% CI, −2.9 to −1.3 g; P < .001). Neonates exposed to prenatal smoking throughout pregnancy had significantly lower body mass (P < .001), FM (P < .001), and FFM (P < .001) compared with those not exposed to smoking. However, neonates of mothers who smoked only before late pregnancy had no significant differences in body mass (P = .47), FM (P = .43), or FFM (P = .59) compared with unexposed offspring. Conclusion Exposure to prenatal smoking leads to systematic growth restriction. Smoking cessation before late pregnancy may reduce the consequences of exposure to prenatal smoking on body composition. Follow-up of this cohort is needed to determine the influence of catch-up growth on early-life body composition and the risk of childhood obesity.