The use of reduced sulfur compounds as electron donors for biological denitrification has the potential to reduce chemical and sludge disposal costs as well as carry-over of organic carbon to the effluent that often occurs with heterotrophic denitrification. Although a number of prior studies have evaluated sulfur oxidizing denitrification (SOD), no prior studies have evaluated particulate pyrite autotrophic denitrification (PPAD) in continuous flow systems. Bench-scale upflow packed bed reactors (PBRs) were set up to compare denitrification rates, by-product production and alkalinity consumption of PPAD and SOD. At an empty bed contact time of 2.9 h, average NO3--N removal efficiencies were 39.7% and 99.9% for PPAD and SOD, respectively. Although lower denitrification rates were observed with PPAD than SOD, lower alkalinity consumption and reduced sulfur by-product formation (SO42-, S2- and SO32- plus S2O32-) were observed with PPAD. Furthermore, higher denitrification rates and lower by-product production was observed for SOD than in prior studies, possibly due to the media composition, which included sand and oyster shells. The results show that both pyrite and elemental sulfur can be used as electron donors for wastewater denitrification in PBRs.