Six isolates of Sclerotium cepivorum Berk were isolated from naturally infected garlic plants collected from different localities of EL-Minya, Assiut and Sohag Governorates. Pathogenicty tests indicated that isolates No.2, 3 and 6 were highly pathogenic to garlic as compared with isolates No.1,4 and 5. Protein of six isolates of S. cepivorum was compared by polyacrylamide gel electrophore-sis (PAGE) and sodium dodecyel sulfate-polyacrylamide gel elec-tophoresis (SDS-PAGE). Protein profiles separated by PAGE, iso-late No. 1 showed the highest number of bands (20 bands), while isolate No. 4 showed the lowest number (15 bands). The number of bands of other isolates was 16 or 17 bands. Protein pro-files separated by SDS-PAGE, isolate No. 5 showed the highest number of bands (19 bands) while isolate No. 3 showed the lowest number of bands (6 bands). The other isolates showed a number of bands ranged from 13 to 17 bands. On the basis of electrophoretic dis-similarities among protein band-ing paterns, isolates were grouped by claster analysis and the results were experessed as phenograms. Grouping the iso-lates based on PAGE analysis was associated with geographic of isolates,however, grouping the isolates based on SDS-PAGE was associated with virulence of isolates