Contamination of eggs with microorganisms that possibly affect eggs quality and transmit pathogens or intoxication to consumers, causing public health hazards. A total of 135 fresh poultry farms eggs were collected randomly from different groceries and markets in Qena city, Upper Egypt. Every three eggs from each market were represented as one egg pooled sample (n =45 pools) Each egg shell and content was examined for their microbiological contents in terms of aerobic plate, enterococci, total coliforms, faecal coliforms and yeast and mold counts /ml, presence of salmonella, Escherichia coli, Listeria, and the presence of total aflatoxins (AFs) levels by enzyme linked immune-sorbent assay (ELISA). The results showed microbial growth on 100%of each (45 shell and content pools) of the examined samples and of all, total aflatoxin contamination was determined to trace amounts in three egg samples (6.7 %) (ranging from 0 .7 to 1.15 ppb).Other samples tested were found to be free from any detectable level of aflatoxins. Among poultry farms hen eggs average values of aerobic plate, enteroccocci and total  yeast and mold  counts / ml of egg shells samples  were 6.16X 10³, 1.6 x10² and 2.50 x 102 cells/ ml, respectively. However in egg contents, the corresponding counts were lower than that of egg shells samples 1.14 X103, - and 5.14 x10 cells/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 15 (33.3%) and 9(20 %) in shells and contents samples, respectively. Also one egg shell sample was contaminated by Listeria monocytogene and salmonella negative. It is concluded that eggs sold in Qena city were of good quality, although occurrence of some pathogenic microorganisms. Therefore, it is recommended that poultry farm hen eggs should not be consumed raw.