Our aim was to determine the effect of intestinal transection and resection on the prevalence of enteric flora and evaluate whether any such changes alter luminal SCFA and lactic acid content. Dogs underwent either 50% proximal (PR, N = 6) or distal (DR, N = 7) resection, distal resection with bypass of the ileocecal junction (DRBP, N = 9) or midpoint transection alone performed to serve as the appropriate control for luminal sampling for either proximal (PTC, N = 6) or distal (DTC, N = 7) resection. Studies were performed every four weeks for 12 weeks. Both jejunum and ileum had >10(5)/ml aerobic bacteria, most commonly E. coli. Streptococcal species were more common in the normal jejunum than ileum but were found in the ileal remnant after PR. Significant (>10(5)) anaerobic growth occurred infrequently in the jejunum, and DR did not increase anaerobic growth in jejunum unless DRBP was performed (93% vs 62% DR, 45% DTC, 20% normal jejunum, P < 0.05). Clostridium species increased significantly in the jejunal remnant after DRBP. Significant anaerobic growth occurred infrequently in normal ileum but increased after PR (89% vs 50% PTC, P < 0.05). Flora normally found in the jejunum tended to increase in the ileum after PR. Jejunal SCFA increased after DRBP (3126 +/- 577 microg/ml vs 1600 +/- 301 DTC, P < 0.05) but not DR (1791 +/- 321 microg/ml). Significant (>10(5)) anaerobic bacterial growth was associated with increased SCFA content (2717 +/- 381 vs 1029 +/- 170 microg/ml, P < 0.05) and the presence of lactic acid (30% vs 5%, P < 0.05), but there was no correlation between the presence of specific bacteria and SCFA and lactic acid. Following resection of the proximal small intestine, the intestinal remnant tends to assume the bacteriologic characteristics of the resected segment. Following a distal resection, the presence of an intact ICJ protects against the proliferation of a flora characteristic of the distal intestine; resection with bypass of the ICJ results in the appearance of coliforms in the jejunal remnant. These changes in enteric flora do not correlate with content of specific SCFA and lactic acid in the small intestine.