In this study, the effects of milk fat content (0%, 2% and 3.5%) and starter culture (autochthonous or commercial) on physicochemical properties, degree of proteolysis, antioxidant activity and viability of Lactobacillus acidophilus, within 21 days storage of probiotic yogurt at 5 ± 1 °C were investigated. Statistical analysis showed that the type of starter culture had a significant effect (P < 0.05) on proteolysis and antioxidant activity, in such a way that both of them were increased until the 14th day of storage but they decreased after this period. Similarly, the pH value of all samples decreased during storage time. It ranged from 3.84-4.34 and 4.18–4.43 for yogurt samples made by autochthonous and commercial starter culture, respectively. According to the results, the survival of Lactobacillus acidophilus decreased during storage time (P < 0.05), although it stood at recommended levels for health effects (at least 106 cfu/ml in traditional yogurt). Milk fat content did not have significant effect on the survival of probiotic organisms (P < 0/05).