Cotinine is the most abundant metabolite of nicotine and is used as the primary indicator for tobacco exposure. Cotinine is typically quantified in human biological matrices using HPLC-MS/MS and GC-MS. However, due to selectivity problems inherent with biological fluid analysis HPLC-MS/MS extraction methods usually require solid phase extraction in order to remove interfering compounds. Published GC-MS methods lack the sensitivity and selectivity requirements necessary to detect cotinine at low ng/mL levels present in those exposed to tobacco smoke. In this work we report a novel method to quantify cotinine in human plasma and urine utilizing a selective and sensitive GC-MS/MS method following a simple supported liquid-liquid exchange extraction (SLE). The method can be used to precisely track the level of tobacco smoke exposure for clinical research applications.