Background: We previously investigated fecal flora of the pouch after total proctocolectomy using terminal restriction fragment polymorphism analysis. Although the results of the cluster analysis demonstrated clearly that bacterial populations, including an unidentified bacteria generating a 213-bp PCR fragment, moved toward a colon-like community in the pouch, it did not track changes in the individual species of fecal bacteria. Aims: The aim of the present study was to estimate genome copy number of ten bacterial species, clusters, groups, or subgroups (including the bacteria generating 213-bp fragment in the previous study) in feces samples from pouches at various times following ileostomy closure. Methods: A total of 117 stool samples were collected from patients with ulcerative colitis after surgery as well as healthy volunteers. We used real-time polymerase chain reaction of the 16S rRNA gene to estimate genome copy numbers for the nine bacterial populations and the bacteria generating 213-bp fragment after identification by DNA sequencing. Results: We demonstrated a time-dependent increase in the number of anaerobic and colon-predominant bacteria (such as Clostridium coccoides, C. leptum, Bacteroides fragilis and Atopobium) present in proctocolectomy patients after stoma closure. In contrast, numbers of ileumpredominant bacterial species (such as Lactobacillus and Enterococcus faecalis) declined. Conclusions: Our data confirm previous findings that fecal flora in the pouch after total proctocolectomy changes significantly, and further demonstrate that the number and diversity of ileal bacteria decreases while a more colon-like community develops. The present data are essential for the future analysis of pathological conditions in the ileal pouch.