New and improved methods for collecting neonatal meconium samples, preparing meconium specimens for testing and for chemically analyzing neonatal meconium samples to determine their chemical composition are provided. A novel extraction method is employed in accordance with the invention to provide a non-aqueous, concentrated "cocktail" meconium extract containing substantially all of many possible target analytes in a single extraction step. Preliminary screening by fluorescence polarization immunoassay methods may be performed on the cocktail extract to qualitatively determine the presence of the target analytes in the meconium sample. If a positive preliminary result is obtained, new and improved quantitative GC/MS confirmatory procedures are provided by this invention to unequivocally identify and quantitate the amount of target analyte present in the sample in terms of nanograms of analyte per gram of meconium tested.