Background and Objectives: Enterococci causes many serious and life-threatening infections. Enterococci may be the cause of diarrhea in children. Multidrug-resistant (MDR) Enterococci limits treatment options. So, the aim of our study was to detect the frequency and the antibiotic resistance profile, both phenotypically and genotypically, of MDR Enterococci isolated from the stools of children suffering from gastroenteritis who needed hospitalization. Materials and Methods: Enterococci were isolated from stool samples from children. One hundred ten (110) infants (in patients) with typical signs of gastroenteritis (nausea, vomiting, abdominal pain, diarrhea). The Vitek 2 Compact System is used for identification and antimicrobial susceptibility testing. Drug resistance genes (ermB, aph(3′)IIIa, and tetM) and virulence genes (esp) were identified using molecular techniques. Results: Thirty-six isolates of Enterococci were diagnosed phenotypically by routine lab examination and Vitek2 followed by genotypic characterization by multiplex PCR for three resistant genes: ermB (100%), aph(3′)IIIa (63.9%) and tetM (91.7%) and one virulence gene (esp (25%)). The frequency of Enterococci among studied patients was 32.7% (36/110). Most of the Enterococci isolated from stool were Enterococcus faecuim (86.1%). MDR Enterococci was found to be 94.4% (34/36) in total isolates. Conclusion: MDR Enterococci was isolated in community acquired diarrhea in young aged (less than 24 months) children. More than one resistance gene: ermB, aph(3′)IIIa, tetM and virulence gene (esp) were detected in isolates. The presence of MDR strains is risky at a young age as it limits treatment options. Drug-resistant genes may be transmitted to a child through a carrier mother or cross infection from the hospital.