Objective: This study investigated distribution of enterococci colonizing intestinal tract of infants, their putative virulence factors and antimicrobial susceptibility patterns. Methods: A total of 82/186 (44.1%) fecal enterococcal isolates were recovered from infants. All enterococci isolates were identified either E. faecalis or E. faecium using culture and PCR. Results: A significant higher intestinal colonization of enterococci was detected among non-hospitalized compared to hospitalized patients with a percentage of (72 % vs. 28%), respectively. E. faecalis was the predominant species isolated from both groups (75.6%). It had also significantly higher virulence factors genes than E. faecium, while E. faecium had higher rates of antimicrobial resistance than E. faecalis. There was no significant factor related to intestinal colonization of enterococci with birth weight, gestational age of mother, gender, type of feeding, present of disease or administration of antibiotics to mothers or infants. Conclusion: This study presents important epidemiological data on the intestinal colonization of enterococci in both hospitalized and nonhospitalized Jordanian infants.