In this study, the microbiological quality of traditionally made yoghurt from Northern Uganda and Western Kenya were analysed. Six samples of typical traditionally fermented milk were randomly collected from traditional cattle keepers from Karamojong (UG 1) and Acholi (UG 2) in Northern Uganda), and Kalenjin in Western Kenya (KE). Analysis was carried out for microbial quality of the collected samples and was assessed using the conventional methods for total aerobic mesophilic bacteria, total coliform, lactic acid bacteria, Staphylococcus aureus, Listeria monocytogenes, yeasts, and mould counts. The results showed that the pH of the samples was low (2.9- 3.6). The mean aerobic mesophilic bacterial counts were 5.14 x 109 cfu/ml. The mean counts for mesophilic lactobacilli ranged from x 106 to x 108, cfu/ml. The mean thermophilic lactobacilli count ranged from x 107, to x 109, cfu/ml. However, the thermophilic lactococci counts ranged from x 106, to x 109, cfu/ml. On the other hand, the Streptococci counts were between x 106 to x 108 cfu/ml. The mean counts for the non-Sorbitol E. coli was 3.87 x 103 cfu/ml. The results suggest that although the pH of the yoghurt made in the Acholi and Karamojong (Northern Uganda) and in Kalenjin (Kenya) areas was low, the level of bacteria, yeast, and mould counts indicated poor microbiological quality control. This poses public health concerns. Therefore, attention of the appropriate government agencies is needed to ensure that environment of yogurt produced in a traditional setting in most appropriate condition to reduce contamination.