The objective of the study was to determine the effect of storing time on the count of characteristic micro-flora in yoghurts with amaranth seeds and oat grains added. Two types of fermented milk drinks were produced: traditional yoghurt and bio-yoghurt containing potentially probiotic bacteria. After the incubation, the yoghurts were stirred and amaranth seeds or oat grains were added in the amount of 3%. The following types of additives were applied: amaranth in the form of whole, ground and extruded seeds, and oat in the form of whole and ground grains. After the 1^st, 3^rd, 7^th and 14^th day of storing the products, their analysis was performed. It included the determination of counts of the following bacteria: S. thermophilus and L. delbrueckii bulgaricus in the traditional yoghurts, and Bifidobacterium sp., L. acidophilus, S. thermophilus in the bio-yoghurts. The active acidity of products was determined by measuring their pH value. The addition of amaranth seeds and oat grains did not statistically significant impacted the analyzed parameters of yoghurts and bio-yoghurts. It was proved that, in the both cases, the level of L. delbrueckii ssp. bulgaricus and S. thermophilus bacteria slightly increased during the 3 days of storing, and, than, decreased reaching the lowest value on the 14^th day of storing. Those changes were statistically significant for all the types of yoghurts. During the storing period, the count of lactobacilli decreased slower than of streptococci. As for the bio-yoghurts, it was found that the count level of Bifidobacterium sp., L. acidophilus, and S. thermophilus slightly varied between the first and the third day. The number of these types of micro-organisms decreased statistically significantly between the 7^th and 14^th day of storing. Among the evaluated bacteria, the highest fall in the count of viable micro-organisms was stated for the Bifidobacterium sp. bacteria. The decrease in the number of bacteria in yoghurts and bio-yoghurts during their storing was connected with the simultaneous increase in their acidity. Although the number of bacteria decreased during the storing period, the yoghurts and bioyoghurts with the amaranth seeds and oat grains added were characterised by a high level of the distinctive micro-flora pursuant to instructions under FIL/IDF.