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This study aimed to evaluate the probable public health hazard imposed by bovine milk in relation to aflatoxin M1 (AFM1) and Coxiella burnetii in the West of Iran. The assessment of AFM1, using an ELISA test, indicated 62.22% and 21.11% of 45 samples of raw and pasteurised milk were above the permissible content of Codex and Iranian standard levels, respectively. Further, anti‐C. burnetii antibody was detected in 63.04% of bulk tank milk samples, with six samples harbouring the bacterial genome. High AFM1 contamination levels and an endemic pattern of Q fever warrant continuous surveillance programmes in the studied region. [ABSTRACT FROM AUTHOR]