A model that predicts the fate and transport of pathogens throughout the entire sanitation service chain, using readily available information from onsite and centralized components of sanitation systems is presented. The development, sensitivity, and application of the model are reviewed. A systematic review of the literature was conducted to estimate pathogen reduction in different onsite sanitation technologies with respect to their design and the mode of operation. Findings of the review are included. The population practicing open defecation and the population practicing safe emptying and conveyance of fecal sludge from onsite pit latrines and septic tanks were the two most sensitive inputs in the model in terms of predicting overall pathogen reduction. Results from running the onsite component of the model indicate that improved sanitation facilities, particularly dual pit/tanks could have a large influence on overall pathogen reduction and the use of flush water in onsite facilities may not necessarily translate to increased efficacy and efficiency in terms of pathogen reduction. As a result of running the centralized component of the model, there is evidence that to adequately control all four pathogen groups (bacteria, viruses, protozoa and helminths), treatment facilities need to address both the treatment of wastewater and sludge/solids residuals. The results of this thesis will support policymakers, engineers, and sanitation safety planners who may be unsure about which technologies to use in order to maximize public health benefits, due to a lack of knowledge about pathogen removal efficiencies in sanitation technologies, especially in developing countries, where data gaps can be immense.