Total no. of patient (100) stool samples were collected, during the period from February to the end of May of 2008, for children under two years old suffering from non-bloody and bloody diarrhea at (Children Welfare Teaching Hospital) in Baghdad. The study evaluates the relationship between etiological agent of diarrhea and sex, age group, type of feeding, presence of blood in stool of the patients. All samples were examined microscopically to identify parasitic agent and serological test for Rotavirus to identify viral infection, also biochemical and serological tested for specimen's culture on different culture media and antibiotic sensitivity test. Results show from 100 cases 64] represents the etiological agent of diarrhea and the most common of this agent was Rotavirus represent (37.5 %), respectively then Entamoeba histolytica (21.9 %), other agents were include Proteus (12.5 %), Enteropathogenic E.coli (10.9 %), Citrobacter braakii (7.8 %), Salmonella typhi (6.3 %), and Giardia lamblia (3.1 %). The remaining 36 isolates represent of unknown etiological agent for another's pathogen.The prevalence ratio of infection in male (75.0 %) was more than in female (25.0 %), in the first year of age especially in the age group (0-6) months (42.2 %). children depending on artificial feeding represent about (57.8 %) higher natural and mixed feeding, the bloody diarrhea associated with Entamoeba histolytica (57.1 %) in contrast to some etiological agent of non-bloody diarrhea. Eleven types of antibiotics were used for sensitivity test show all serotype of Enteropathogenic E.coli and Salmonella typhi are sensitive to Imipenem and Ciprofloxacin. The predominant serotypes of Enteropathogenic E.coli which represent serotype O111 and serotype O125 these strains show resistance to Cefotaxime (CTX), Trimethoprim-sulfamethaxazole (SXT), Ampicillin (AM), Metronidazole (MET), Cefoperazone (CEP), Cefixime (CFM), also the serotype O111 resistance to Gentamicin (CN) represent (45.0 %), while the most resistance of Salmonella was to Amikacin (100.0 %). This may reflect the fact that the increased resistance in older children and adult may be associated with the development of immunity or the loss of receptors for some specific adhesion. In Iraq Rotavirus infection is estimated to account for (10-29 %) in early childhood, While in neighboring countries the rate ranges between (19-46 %). The study show infected males more than female and the highest diarrheal infection was caused by Rotavirus, the Imipenem and Ciprofloxacin antibiotic was the most effective one against pathogenic strains of Enteropathogenic E.coli and Salmonella typhi while all isolates were resistant to Trimethoprim-Sulfamethaxazole, Ampicillin, Metronidazole.