The objective of this study was to investigate the microbial contamination of red meat (cow and sheep) and chicken in slaughterhouses from Kermanshah province using Hazard Analysis Critical Control Points (HACCP) system. To enumerate the investigated microorganisms, including total bacterial count, Escherichia coli, Staphylococcus aureus, Salmonella spp., and Listeria monocytogenes, in the slaughter line of cow, sheep, and chicken, plate count agar, eosin methylene blue, Baird-Parker agar, Salmonella Shigella agar, and PALCAM Listeria selective agar were utilized, respectively. In the final washing and cooling steps of cow and sheep carcasses, the total viable count was significantly lower and higher than other steps, respectively (P < 0.05). At the stage of cooling the carcass and emptying the intestines and viscera, the lowest and highest counts of E. coli, Salmonella spp. and L. monocytogenes were isolated. The results of this study showed that the counts of investigated pathogens, including L. monocytogenes (2.25 log CFU/g), Salmonella spp. (2.31 log CFU/g), E. coli (2.41 log CFU/g), and S. aureus (2.18 log CFU/g) significantly decreased after storing chicken in cold conditions (P < 0.05). The results of this study indicated that the microbial quality of red meat (cow and sheep) and chicken meat samples at the end of the production line and before distribution was acceptable.