Antimicrobial therapy can increase the colonization density of gastrointestinal vancomycin-resistant enterococci (VRE). Among previously VRE-colonized patients, we evaluated VRE colonization before and after initiation of antimicrobial therapy by means of polymerase chain reaction (PCR) and culture. Perianal swab samples were obtained at admission to the hospital and after receipt of antimicrobial therapy. At admission, 12 (21%) of 56 patients were culture positive, and 17 (30%) had vanA or vanB genes detected by PCR. Culture results showed that 25 (86%) of 29 culture-negative patients from whom a second swab sample was obtained remained culture negative, 2 (6.9%) had a relapse of colonization with a strain related to the previously colonizing strain type (2 and 6 days after admission), and 2 (6.9%) tested positive for a previously undetected strain type (16 and 19 days after admission). PCR at admission detected VRE in 1 of the 2 patients who later relapsed. Patients with negative results of culture of the initial swab sample and of PCR were unlikely to relapse after receipt of antimicrobial therapy.