This study evaluated the presence of biogenic amines in fermented cow’s and goat’s milks containing probiotic bacteria, during the first 10 days of chilled storage (4 ± 2°C), when the probiotic strains are most viable. The overall acceptance of both fermented milks, produced using the same starter culture and probiotics, was tested. In both products, the initially high levels of tyramine (560 mg kg −1 means for both fermented milks), the predominant biogenic amine, increased during the storage period, which may be considered this amine as a quality index for fermented milks. The other principal biogenic amines (putrescine, cadaverine, histamine, and spermidine) were produced on days 1–5 of storage, and thereafter decreased. At the end of the 10th day, these amines, respectively, showed values of fermented cow’s milk 20.26, 29.09, 17.97, and 82.07 mg kg −1; and values of fermented goat’s milk 22.92, 29.09, 34.85, and 53.85 mg kg −1, in fermented cow’s and goat’s milk. Fermented cow’s milk was well accepted compared to fermented goat’s milk. The results suggested that the content of biogenic amines may be a criterion for selecting lactic acid bacteria used to produce fermented milks.