The formation of cotinine, the main proximate metabolite and a biomarker of nicotine exposure, is mediated primarily by CYP2A6. Our aim was to determine if higher cotinine levels in young children exposed to secondhand smoke (SHS) are a result of age-related differences in pharmacokinetics. Forty-nine participants, 2 to 84 months old, received oral deuterium-labeled cotinine, with daily urine samples for up to 10 days for cotinine half-life measurement. DNA from saliva was used for CYP2A6 genotyping. The estimate of half-life using a mixed effect model was 17.9 hrs (95%CI: 16.5, 19.3), similar to that reported in adults. There was no statistically significant effect of sex, race, age, or weight. Children with normal activity CYP2A6*1/*1 genotypes had a shorter half-life than those with 1-2 reduced activity variant alleles. Our data suggest that higher cotinine levels in SHS-exposed young children compared to adults are due to greater SHS exposure rather than different cotinine pharmacokinetics.Clinical Pharmacology & Therapeutics (2013); accepted article preview online 29 May 2013. doi:10.1038/clpt.2013.114.