This investigation was run to compare the microbiological quality between raw and pasteurized milk yoghurt. A total of 70 raw and pasteurized milk yoghurt samples (35 samples of each) were collected from small dairies and supermarkets in Assiut City, Egypt. All samples were investigated to determine the Enterococci, yeasts and molds, Staphylococcus aureus, coliforms, faecal coliforms and E. coli count. Also, for detection of anaerobes. In raw milk yoghurt samples the incidences of Enterococci, yeasts and molds, coliforms, faecal coliforms and E. coli were 40, 82.9, 62.9, 57.1 and 54.3%, respectively; while, for pasteurized milk yoghurt samples, the incidences were 22.9, 77.1, 2.9, 2.9 and 2.9%, respectively. On the other hand, Staphylococcus aureus and anaerobes could not be detected in this study. The microbiological results in this study were compared with the limits of Egyptian Organization Standards.