This study was carried out to determine the sources of microbial contamination in Doogh production line during a year in a dairy factory. Samples were taken from different control points from the beginning to the end of the production line including raw milk, pasteurized milk, water, culture, Doogh yoghurt, pasteurized Doogh, packed Doogh, filler and filling air duct, storage hall for pasteurized Doogh, and filling and storage rooms. The microbial analysis of the samples was performed to determine the total count of microorganisms, mold and yeast, coliforms, E. coli, Psychrophilic and thermophilic microorganisms, lactic acid bacteria and coagulase positive staphylococci in accordance with national standards of Iran. The results showed that Doogh health quality depends on the quality of raw milk, the adequacy of heat treatment, microbial quality of the ingredients and packaging materials, doing suitable CIP and disinfectantion of processing surfaces and factory environment. The results indicate that the assessment of critical control points and the organization of automatic control systems are necessary in order to eliminate or minimize the risk of microbial contaminats.