The effect of growth promotants (bacitracin, virginiamycin, and flavomycin) on the genetic population of Enterococcus faecium isolated from a commercially integrated poultry farm was examined. A total of 551 E. faecium were isolated from chick boxliners (n = 16), litter (n = 334), feed (n = 67), and carcass rinse (n = 134) samples from four chicken houses. Two houses on the farm were control houses and did not use any antimicrobials while two other houses on the farm used flavomycin, virginiamycin, and bacitracin during six different chicken grow outs. BOX-PCR and pulsed-field gel electrophoresis (PFGE) results indicated that E. faecium strains had a high degree of genetic diversity as overall clustering was independent of source, house, or grow out. Similarity of ≥60% for the majority of BOX-PCR genogroups and ≥80% for the majority of PFGE genogroups was observed for a subset of carcass rinse samples (n = 45) examined. Seventy-nine percent (19/24) of isolates in BOX-PCR genogroup 2 also clustered in PFGE genogroup 2, although no association between the isolates and house or grow out was observed. These results suggest that E. faecium from chicken are genetically diverse and that growth-promoting antimicrobials do not affect the genetic population of E. faecium.