Hydrocarbon biomarkers in highly mature Precambrian rocks have the potential to provide important information about the diversity ecology, and evolution of early life, but studying them presents special analytical challenges. Extractable hydrocarbons are present in Archean and most Paleoproterozoic sedimentary rocks in such trace concentration that even slight contamination from petroleum-derived materials in situ or during drilling, storage, sampling, handling and laboratory analysis would compromise the results and, thereby, any consequent inferences. Here we report protocols that we have developed for the analysis of cores from several recently completed deep-time scientific drilling initiatives. By paying special attention to cutting, cleaning, crushing and extraction, it is possible to significantly reduce laboratory blanks to acceptable levels. When these methods are utilized, meaningful variations in the patterns of biomarkers over stratigraphic and lithologic boundaries provide compelling evidence for syngeneity.