Technical Abstract: Concern has greatly increased about the potential for contamination of water, food, and air by pathogens present in manure. We evaluated pathogen reduction in liquid swine manure in a multi-stage treatment system where first the solids and liquid are separated with polymer, followed by biological nitrogen (N) removal using nitrification and denitrification, and then phosphorus (P) extraction through lime precipitation. Each step of the treatment system was analyzed for Salmonella and microbial indicators of fecal contamination. Before treatment, mean concentrations of Salmonella, total coliforms, fecal coliforms, and entrerococci were 3.89, 6.79, 6.23 and 5.73 log10 colony forming units cfu)/mL, respectively. The flushed manure contained 10,590 m/L TSS, 8,270 mg/L COD, 688 mg/L TKN and 480 mg/L TP, which were reduced >98% by treatment. Results showed a consistent trend in reduction of pathogens and microbial indicators as a result of each step in the treatment system. Solid-liquid separation decreased their concentrations by 0.5 to 1 log10. Additional biological N removal treatment with alternating anoxic and oxic conditions achieved a higher reduction with average removals of 2.4 log10 for Salmonella and 4.1 to 4.5 log10 for indicator microbes. Subsequent P treatment decreased concentration of Salmonella and pathogen indicators to undetectable level (<0.3 log10 cfu/mL) due to elevated process pH (10.3). Our results indicate that nitrification/denitrification treatment after solids separation is very effective in reducing pathogens in liquid swine manure and that the phosphorus removal step via alkaline calcium precipitation produces a sanitized effluent which may be important for biosecurity reasons.