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The aim of this study was to monitor the quality and mycobiota composition of table eggs during storage period. The most significant changes in the egg weight and water activity were observed on Day 7. To identify the mycobiota present on the eggshell by PCR method, a newly designed procedure for the extraction of fungal DNA based on a combination of commercial isolation kit, proteinase K and ultrasound was implemented. Identified mold genera included Penicillium spp., Cladosporium spp., Fusarium spp. and Alternaria alternata group. Their ratio varied considerably during storage with the dominance of Penicillium spp. on Day 14.