Background: Aflaxions are a group of chemically toxic fungal metabolites produced by species of the genus Aspergillus. Nuts can be contaminated by fungi, resulting in the production of mycotoxins. The present study was performed to investigate the ability of selenium-fortified yogurt to counteract the adverse effects of consuming 3% experimental nuts (pistachios, cashews, walnuts, almonds and hazelnuts) contaminated with aflatoxins in experimental rats. First, the total aflatoxins concentrations were estimated in fresh nuts, and in nuts after 6 months of storage, and seleniumfortified yogurt was prepared. Rats were classified into a negative control group (fed a standard diet with a 3% mixture of fresh safe nuts), a positive control group (fed a standard diet with a 3% mixture of nuts contaminated with aflatoxins after storage at 25 °C for 6 months) and treated groups that fed on pistachios with selenium-fortified yogurt, cashews with selenium-fortified yogurt, walnuts with yogurt fortified with selenium, almonds with selenium-fortified yogurt and hazelnuts with selenium-fortified yogurt (fed a standard diet with 3% individual nuts contaminated with aflatoxins and 160 ml/kg body weight of selenium-fortified yogurt daily through a stomach tube). Results: The negative effects of aflatoxins on weight gain and food intake were reversed by selenium-fortified yogurt. This yogurt also led to a significant decrease in serum cholesterol, TG, LDLc, VLDLc, total lipids, phospholipids, glucose and atherogenic indexes (CHO/HDLc and LDLc/HDLc) and an increase in serum HDLc, haemoglobin, PCV, liver TG and glycogen at p < 0.05. In addition, the study showed a significant decrease in liver cholesterol and total lipids compared to the positive control rat group, which consumed 3% mixed nuts contaminated with aflatoxins and simultaneously restored these parameters to be close to those in the control group. The results were corroborated by histopathological examination of the liver and kidneys. Conclusions: The most prominent conclusion is that selenium-fortified yogurt reduces side effects from consumption of nuts contaminated with aflatoxins. It is recommended to consume functional selenium-fortified yoghurt for its nutritional values and for alleviating the harmful effect of aflatoxins in nuts.