Background Antimicrobial resistance is an increasing threat to health systems which leads to treatment failure, high treatment costs and increased mortality. Infections due to extended spectrum beta-lactamase (ESBL) and carbapenemase producing Enterobacteriaceae(CPE) impose a major global issues, because they are usually resistance to multiple antimicrobial agents. Data on the fecal ESBL producing Enterobacteriaceae (ESBL-PE) and CPE in developing countries including Ethiopia is limited mainly due to resource constraints. Thus, the aim of this study was to determine the prevalence of MDR, ESBL and CPE among patients with gastrointestinal complaints at the University of Gondar Comprehensive Specialized Hospital, Gondar; Northwest Ethiopia.Materials and Methods A Hospital based cross-sectional study was conducted among 384 patients with gastrointestinal complaints from January - April 2019 at the University of Gondar Comprehensive Specialized Hospital. A stool sample was aseptically collected and inoculated on MacConkey agar plate. After getting pure colonies, biochemical testing and antimicrobial susceptibility testing were done following standard microbiological techniques. ESBL production was screened by using ceftazidime and cefotaxime and confirmed using a combined disk diffusion test based on CLSI 2019 guidline. Carbapenemases were screened by meropenem disc and confirmed by modified carbapenem inactivation method. Data was checked, cleaned and entered using Epi-Info version 7.1 and transferred to SPSS version 20 for analysis. P-value <0.05 at 95% CI was considered as statistically significant.Result Out of the 384 study participants, 404 Enterobacteriaceae were isolated. Among these, 196 (48.5%) were MDR. The overall prevalence of fecal ESBL and CPE were 66(16.3%) and 4(1%) respectively. Of the total ESBL-PE, E.coli 41/66(62.1%) and K.pneumoniae 18/66(27.3%) were the most predominant isolates.Conclusion Finding high rate of MDR Enterobacteriaceae,ESBL-PE and CPE require strict infection control measures and careful selection of empirical therapy in the study area. Therefore, active surveillance with large sample size and better infection prevention and control is needed.