Nowhere is the importance of accurate determination of recent human fecal contamination greater than in the tropics. The diversity of waterborne diseases and their severity is greatest in tropical environments. Since most of the countries in tropical climates are underdeveloped, with large populations that are undernourished, ill-housed, with poor medical services, waterborne diseases may have a much greater effect on public health in the tropics than in temperate areas. Universally, tropical areas accept water maximum contaminant levels developed by temperate nations, despite the obvious differences in tropical climates. High densities of total and fecal coliform bacteria have been detected in pristine streams and in groundwater samples collected from many tropical parts of the world, even in epiphytic vegetation 10 m above ground in the rain forest of Puerto Rico. Nucleic acid (DNA) analyses of Escherichia coli from pristine tropical environs has indicated that they are identical to clinical isolates of E. coli. Many tropical source waters have been shown to have enteric pathogens in the complete absence of coliforms. Diffusion chamber studies with E. coli at several tropical sites reveal that this bacterium can survive indefinitely in most freshwaters in Puerto Rico. An evaluation of methods for the enumeration of fecal coliforms showed that currently used media have poor reliability as a result of large numbers of false positive and false negative results when applied to tropical water samples. Total and fecal coliform bacteria are not reliable indicators of recent biological contamination of waters in tropical areas. Fecal streptococci and coliphages in tropical waters violate the same underlying assumptions of indicator assays as the coliforms. Anaerobic bacteria like Bifidobacterium spp. and Clostridium perfringens show some promise in terms of survival, but not in ease of enumeration and media specificity. The best course at present lies in using current techniques for direct enumeration of pathogens by fluorescent staining and nucleic acid analysis, and developing tropical maximum contaminant levels for certain resistant pathogens in tropical waters.