This study was conducted to assess the temperature profile and corresponding pathogen inactivation in lab-scale compost piles. The variation in temperature at different locations of piles and E. coli concentrations was evaluated. The experiment design included plastic containers of different height filled with organic feedstock. Cotton balls soaked with pathogens (E. coli and E. coli O157:H7) were placed inside the feedstocks at various depths. Subsequently, change in pathogen concentrations, feedstock characteristics, and temperature was monitored over time. Observations showed fluctuation in temperature of piles. The peak temperature (> 50 °C) was reached after two weeks of expertiment. The concentrations of E.coli and E. coli O157: H7 at different depths varied among piles during the 35 days of experiments. The reductions in E. coli concentrations ranged 1- 4 orders of magnitude. In certain piles, reduction in E. coli concentrations was followed by increased in E. coli levels indicating the possibility of perturbation of bacteria in the feedstock potentially at low temperature. We anticipate these preliminary results will provide additional insights on pathogen inactivation in compost system. The approach used here can be implemented at field-scale compost piles for assessing pathogen inactivation during compost process under field conditions.