The article presents the results of complex study of cotton-seed cake from the Republic of Tajikistan, including the determination of content of mycotoxins, the analysis of exposure to microscopic fungi and the assessment of the potential of their toxin formation. The ability to produce mycotoxins was established for 11 species of micromycetes belonging to the genus Aspergillus, Penicillium, Fusarium, Scop-ulariopsis, and Trichothecium. Alternariol, zearalenone, fu-monisins, aflatoxin B1, sterigmatocystin, ochratoxin A, citrinin and emodin were found in the composition of the cotton-seed cake. Prospects for further research and the practical significance of the results are discussed.