Aflatoxins (AFs) are naturally toxic compounds produced by a specific type of fungi, which subsequently contaminate foods and animal feeds, potentially carcinogenic to humans. This study aimed to assess the effect of lactation period and parity order on Aflatoxin AFM1 and the association between them through smallholder dairy farms in addition to aflatoxin M1 in local cheese “DANGKE” and Aflatoxin B1 in animal feed samples from Enrekang, South Sulawesi, Indonesia. A total of 39 raw cow milk samples and 12 and 16 roughage and concentrated feed samples were randomly obtained from smallholder dairy farms in Enrekang and they were examined in terms of AFM1 and AFB1 using Enzyme-Linked Immunosorbent Assay (ELISA) method. The prevalence of Aflatoxin B1 in roughage animal feed was 8.33%, with a concentration range of 7.32µ/kg above the limit of detection. The concentrated feed has a different amount of Aflatoxin B1 according to the type of feed used in the farm ranging from 6.04 to 58.74µ/kg with a mean of 27.8µ/kg and representing 37.5% for all concentrated feed samples. The prevalence of Aflatoxin M1 in milk revealed that 69.2% of samples were positive ranging from 3.08±4.35 to 7.95±0.24µ/kg with a mean 5.05±3.50µ/kg above a limit of detection. All samples from cheese showed negative results for AFM1. However, 3(50%) of positive concentrated feed samples exceeded the European Union (EU) regulation of 20µ/kg for dairy animal feed, the roughage feed samples and all of the concentrated feed samples were under Indonesian National Standard (SNI) of 200µ/kg, these three samples namely commercial concentrate and rice bran they include about 57.18, 30.98 and 58.74µ/kg, respectively. Therefore, all raw milk-positive samples were above the limits of the Indonesian national standard of 0.5µ/kg, and above EU and USA limits of 0.05 and 0.50 µg/kg, respectively for raw cow milk. The results showed that no relation between the amount of aflatoxin M1 and lactation period and parity order (P˃0.05). In contrast, the interaction of lactation period and parity order significantly (P<0.05) affected aflatoxin M1 in raw cow milk. Further research is needed to explore the association between the aflatoxin lactation period and parity order. The study revealed a high prevalence of aflatoxin contamination in animal feeds and raw cow milk, suggesting a potential health risk to consumers. Therefore, it is vital to increase awareness and knowledge on Aflatoxin, proper handling, storage, and monitoring of feeds among the stakeholders in the dairy value chain.