The temperature-phased anaerobic biofilter (TPAB) process is a new high-rate anaerobic treatment system that includes a thermophilic biofilter connected in series to a mesophilic biofilter providing for two-temperature, two-phase treatment. Three TPAB systems with thermophilic:mesophilic reactor size ratios of 1:7, 1:3, and 1:1 were operated at system hydraulic retention times (HRTs) of 24, 36, and 48 hours at temperatures of 56 degrees C in the thermophilic phase and 35 degrees C in the mesophilic phase. The three TPAB systems achieved soluble and total chemical oxygen demand (GOD) reductions in excess of 97% and 90%, respectively, for a synthetic milk substrate over a range of system COD loadings from 2 to 16 g COD/L/d. There was little difference in performance between the three TPAB systems based on COD reduction and methane production, making it feasible to use a smaller thermophilic first phase in the TPAB system. At the 48-hour system HRT, the 6-hour thermophilic phase biofilter reached saturation loading at a COD load of 48 g/L/d. After further increases in organic loading, the methane production decreased in the thermophilic first phase and increased in the corresponding mesophilic second phase while levels of n-valeric and butyric acids increased significantly. It is proposed that a microbial population shift occurred in the thermophilic first phase at high organic loadings at low HRTs. Although a decrease in methane production from the thermophilic phase was observed, the performance of the overall two-stage TPAB system did not decline. The TPAB systems were observed to outperform single-stage anaerobic filters operated at equivalent HRTs and organic loadings.