Aflatoxin M1 contamination was examined in raw milk (3716) and UHT milk (706) samples collected from farms of eastern Croatia and markets of central Croatia from February to July 2013. A maximal mean AFM1 of 1135.0 ng/L was measured in raw milk in March. The AFM1 levels exceeded the European Union maximum residue permitted amount (EU MRL) in 45.9% raw and 36.2% UHT milk samples in February. In total, AFM1 levels exceeded the EU MRL values in 27.8% of raw and 9.64% of UHT milk samples. A slight decrease in the number of samples exceeding the EU MRLs was recorded in the period March to June. The results showed significant statistical differences between the mean AFM1 concentrations of raw and UHT milk samples collected during February, March, May and June (P < 0.05, all). Also, statistical differences in AFM1 concentrations were found between months for raw and UHT milk (P < 0.001, both). In conclusion, the frequency of control of feed and milk samples should increase and should strive to educate breeders and those involved in milk production about the harmful effect of aflatoxins to animal feed.