A growing beneficial reuse of biosolids in agriculture has led to concerns about potential contamination of water resources and the food chain. In order to comprehend the potential risks of transmission of diseases to the human population, an advanced quantitative risk assessment is essential. This requires good quantitative data which is currently limited due to the methodological limitations. Consequently, further development and standardization of methodologies for the detection, enumeration and viability assessment of pathogens in biosolids is required. There is a paucity of information on the numbers and survival of enteric virus and protozoan pathogens of concern in biosolids. There is a growing urgency for the identification of more reliable alternative indicators, both index and model microorganisms, which could be used for potential public health risk assessment. In this review, we have summarized reported literature on the numbers and fate of enteric pathogens and indicators in biosolids. The advantages and limitations of the use of conventional and alternative index and model microorganisms for the prediction of pathogen presence in biosolids are also discussed.