Organic markers, such as sterols and ketones, were used to assess sewage contamination in sediments from the Santos Bay, SP, and its continental shelf. These compounds were analyzed by GC/FID after soxhlet extraction, clean up and derivatization. The concentration of coprostanol and ratios between selected sterols were used to evaluate fecal contamination. The stations located in the mid-western part of the Santos Bay presented organic matter from sewage due to the input of fecal material from the city of Santos by submarine sewage outfall. Stations located at the continental shelf did not present fecal contamination. Coprostanol levels in sewage outfall stations were higher in comparison to other Brazilian coastal areas, except Guanabara Bay/RJ, and could be related to the fraction of the population without sewage treatment.