Abstract: The objective of this study was to investigate the prevalence and to track associated risk factors of antibiotic resistant Salmonella, E. histolytica and G. lamblia in Harar, Eastren Ethiopia. A total of 384 stool samples were collected from Harar Hiwot-Fana Hospital and analyzed in Harari Regional Laboratory. The results of the study revealed that 96(25%), 80(20.6%) and 56(14.6%) of the samples were positive for Salmonella, E. histolytica and G. lamblia, respectively. The antimicrobial sensitivity test showed that all (100%) of the Salmonella isolates were sensitive to ciprofloxacin while 85% were sensitive to nalidixic acid. Of the 56(14.6%) Salmonella isolates, 100, 100, 85 and 71.2% were resistant to ampicillin, tetracycline, trimethoprim-sulfamethoxazole and chloramphenicol, respectively. This study indicated that Salmonella, E. histolytica and G. lamblia were prevalent in Harar and this enterophathogens should be considered routinely in the diagnosis of patients with diarrhoea. Moreover, physicians should also prescribe appropriate drugs either after sensitivity testing or in areas where there are no facilities for culturing and they have to refer updated information on local sensitivity patterns.