Yeasts and molds can grow on or in eggs, causing spoilage. Washed and unwashed eggs (treatments) were collected aseptically on three separate days (replications) from a commercial processing facility and stored for 10 weeks at 4 degrees C. Ten eggs from each treatment were sampled weekly (110 eggs per treatment per replication). Yeasts and molds were enumerated from external shell rinses by plating onto acidified potato dextrose agar. Yeast colonies were picked randomly and stored for subsequent identification by gas chromatographic analysis of fatty acid methyl esters using the MIDI Microbial Identification System. Of 688 isolates analyzed, 380 were identified to genus or species. Genera identified by this method included Candida, Cryptococcus, Hansenula, Hyphopichia, Metschnikowia, Rhodotorula, Sporobolomyces, and Torulaspora. Candida spp. accounted for 84.5% (321 of 380) of the isolate identifications. Candida famata was the most prevalent species (n = 120), followed by Candida lusitaniae (n = 38). A group of 20 isolates was subjected to molecular or biochemical analyses for comparison with the MIDI results. Biochemical tests were performed using automatic and mini systems. Results of biochemical tests and ribosomal DNA sequencing were in agreement for 11 of the isolates, but only 7 of the 20 MIDI-identified isolates were in agreement with the sequencing results. C. famata, an anamorph of Debaryomyces hansenii var. hansenii, was the most commonly identified isolate by all methods. These data indicate that there was limited correlation between results obtained with the MIDI system and the information obtained from molecular databases. However, both systems were able to correctly identify C. famata, the species most often isolated throughout egg storage.