Background: The diagnosis of infectious agents of diarrhea among children is a challenging clinical problem in daily practice. Aim: This study was undertaken to detect some microbial agents among children suffuring from diarrhea below two years in Kirkuk city. Sitting and design: Clinical blocked controlled study on 221 children in Kirkuk city. Materials and methods: by Stool examination using different methods including routine stool examination for bacteria and parasites and some special tests for Rota viruses and other pathogens. Statistical analysis was performed using Chi-square test. Results: From examination of 221 stool samples, only 145(65.59% ) samples were positive for microbial agents, which included:35.29%,23.07% and 7.33 % for protozoan, rotavirus and bacterial infections respectively P<0.05.The common protozoa involve Entamoeba histolytica 19.09 %,Cryptosporidium oocysts 14.47 % and Giardia lamblia 0.90 % P<0.05.Realationship between the distribution of microbial infection in regard of gender and child age was significant in which protozoan infections in males 20.34% was higher than females14.91 %, while it was not significant in regard of Rota-virus and bacterial infections .Also intestinal infections rate 11.73 % was higher among children aging from 19 to 24 months than other age groups reversely to 8.13 % of rotavirus infection that recorded among children aging from one month to 6 months. High rate of rotavirus infection 15.38 % was recorded among children depending on bottle feed comparing to breast and mixed mode of feed P<0.05.While mixed modes of feeding both bottle & breast feeds reveal high rates of intestinal protozoa and bacterial infections, the rates were 14.47 % and 3.7 % respectively P<0.05.The association of microorganism distributions with family member numbers and child family residency were statistically significant P<0.05. Relationships between microbial distributions and socio-economic state of children families, stool consistency, pH and number of feces discharge per day were not significant statistically. Conclusion: microbial infectious agents rates among children below two years old in Kirkuk city were high specially Entamoeba histolytica ,Cryptosporidium parvum and rotavirus.