This Research Communication aims to compare the effect of A1A2 and A2A2 cow milk diets on the biochemical and histological parameters of rats. The rats were divided into four groups and fed with a normal diet, A2 milk powder, A1A2 or A2A2 cow milk diets for 90 d. Blood glucose, kidney function, liver function and lipid profile were examined during the experimental period. The study showed an increase in the body weight of the A1A2 group whereas a slight decrease in the A2A2 group, and blood glucose levels increased from d 0 to day 90 in all experimental groups. However, none of these changes were found to be statistically insignificant (P > 0.05). Moreover, no significant changes were recorded in other parameters (serum glutamic pyruvic transferase and serum glutamic-oxaloacetic transaminase for liver function, bilirubin direct, cholesterol, triglycerides, creatinine and uric acid). The histology of the liver, kidney and pancreas also showed no changes in all groups. Overall, this study revealed no significant difference in the nutritional values of A1A2 and A2A2 milk types and hence equally beneficial for health. Although the present study showed no significant difference in the effect of both milk types in 90 d, further studies might be conducted to evaluate their longer term effects.