A B S T R A C TBackground and Objectives: Pre-requisite programs (PRPs) are "primary conditions and requirements essential for HACCP operations, which are crucial in food safety programs". The present study was conducted to evaluate the impact of implementation of PRPs on the microbial parameters of pasteurized milk (according to the National Standard of Iran). Effectiveness of HACCP operation requirements and efficiency of Good Laboratory Practice (GLP) were also evaluated in control of the above-mentioned microbial parameters. Materials and Methods:According to the approved checklist of the Vice-chancellor in Food and Drug affairs, PRPs of 26 factories were evaluated from March 2014 to March 2015 in two-month intervals, and their total and component scores were obtained along with the microbial parameters of pasteurized milk. Generalized Estimating Equations (GEEs) were used to determine the significance of total score and the impact of its components on controlling microbial hazards.Results: There was a reverse significant relation between the total scores of the PRPs and microbial hygiene indices (total and coliform count) which approves the effectiveness of operating the programs in controlling the mentioned microorganisms. Efficiency of each pre-requisite program was different in controlling the microbial parameters. Good Laboratory Practice (GLP) had a prominent effect on controlling of the index microorganisms of hygienic operations. Overall, the results showed a little probability of contamination with E. coli in the pasteurized milk samples of Fars Province for which the statistical analysis was ignored. Conclusions:The exact operation of PRPs resulted in reduction of microbial parameters in a way that increasing the total score of PRPs led to decrease in microbial parameters of total count (TC), coliforms, molds and yeasts. The findings further suggest the application of this checklist in evaluation and prediction of microbial parameters.