Contamination of Japanese quail eggs (Coturnix coturnix) with microorganisms that possibly affect quail eggs quality and pathogen transmission induced food borne infection or intoxication to consumers which cause public health hazards. A total of 150 quail eggs were collected randomly from different quail farms in Qena city (Upper Egypt), every five eggs were represented as one egg sample (n=30). Each egg shells and contents were examined for their microbiological contents. The results showed that average values of aerobic plate, enteroccocci, total coliforms, fecal coliforms, E.coli, and total  yeast and mold  counts / ml of egg shells samples were 1x10⁴, 7 x10², 5 x10², 1 x10, .784 x10 and 9 x10³ cells/ ml, respectively. However in egg contents, the corresponding counts were lower than that of egg shells samples (7 x10³, 1 x10³, 1.9 x 10, *< 10,   - and 6 x10³cells/ml). Moreover, E. coli was found to be the most prevalent strain recovered from shell but not be detected in contents. The contamination by S. aureus were in 12 (40%) and 5(17%) in shells and contents samples, respectively. Also two egg shell samples were Listeria gray positive, and salmonella negative. Furthermore the identification of molds revealed that 16(53%) and 8(27%) fungi species belonging to 6 genera were isolated from quail egg shells and contents, respectively. Penicillium was the most prevalent genus encounted in egg shells and contents samples comprising 6(20 %) and 4(13%), respectively, of the total fungi.