Residual samples from blood spots (i.e., whole blood spotted onto filter paper) are a useful source for epidemiological screening studies involving newborns. However, the small volume of blood available from residual blood spots complicates the assay. A method for analyzing benzoylecgonine (BZE; the primary metabolite of cocaine) in blood spots, in which the blood spot is eluted with aqueous ammonium acetate-methanol containing N-methyl trideuterated-BZE as an internal standard, followed by high-performance liquid chromatography-atmospheric pressure chemical ionization tandem mass spectrometry using multiple reaction monitoring, has been developed. This approach provides a rapid, direct, sensitive (limit of detection, approximately 2 ng/mL, based on a 12-microL sample size), and highly specific means of determining BZE concentrations in blood spots. We have applied this method for confirmatory analyses in a large epidemiological study of the prevalence of cocaine use during late pregnancy.