Presence of aflatoxin M1 (AFM1) in milk should be continuously controlled in order to protect the population from risks associated with its proven toxicity and carcinogenicity. During recent years, there has been an increase in demand for development of sensitive, accurate, simple and fast method which is reliable for detection of AFM1 at low concentrations found in milk samples. For that purpose, enzyme linked immunosorbent asssay (ELISA), high performance liquid chromatography with fluorescence detector (HPLC-FLD) and high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) were optimized and validated in order to apply them for AFM1 analysis in naturally contaminated milk samples, and to assess the closeness of agreement between results of three different methods. The obtained validation parameters indicate that all three methods are suitable for determination of AFM1 in milk samples. The statistical analysis of variance between the methods and the obtained correlation coefficients indicate that there is a strong correlation between methods. All three methods are satisfactory in meeting the requirements for official control purposes. To the best of author's knowledge, this study represents the first report of an investigation and comparison of ELISA, HPLC-FLD and HPLC-MS/MS methods for determination of AFM1 in naturally contaminated milk samples.