The objective of this research was to perform an exposure assessment of aflatoxin M1 (AFM1) intake through the consumption of milk and yoghurt by the student population in Serbia and Greece. A food consumption survey of milk and yoghurt was performed during the first half of 2018 in the two countries with at least 500 interviewees (aged between 18 and 27 years) per country, covering their dietary habits and body weight based on one-day and seven-day recall methods. Values for the concentration of AFM1 were extracted from published research. Finally, a Monte Carlo analysis of 100,000 iterations was performed to estimate the intake of AFM1 from the consumption of the two dairy products. Results revealed that the estimated average exposure of students to AFM1 was in the range of 1.238–2.674 ng kg −1 bw day −1 for Serbia, and 0.350–0.499 ng kg −1 bw day −1 for Greece, depending on the dietary recall method employed. High estimations for hepatocellular carcinoma (HCC) cases/year/10 5 individuals, depending on the prevalence of Hepatitis B virus surface antigen positive individuals (HBsAg+), were 0.0036–0.0047 and 0.0007–0.0009 for Serbia and Greece, respectively. Presented Margin of Exposure (MOE) and Hazard Index (HI) values indicate increased risk from exposure to AFM1, particularly in Serbia.