Small intestinal bacterial overgrowth (SIBO) was diagnosed by quantitative bacterial culture of duodenal juice samples obtained endoscopically in 41 of 80 dogs that were admitted with chronic diarrhea, vomiting, or weight loss. Thirteen dogs had aerobic bacterial overgrowth, most frequently comprising Escherichia coli, staphylococci, and enterococci, and 28 dogs had mixed anaerobic overgrowth, most frequently including Clostridium and Bacteroides spp. Affected dogs comprised 23 breeds, including 10 German Shepherd Dogs and median age at diagnosis was 2 years (range, 6 months to 11 years). High serum folate and low serum cobalamin concentrations had fair specificity (79 and 87%, respectively), but low sensitivity (51 and 24%, respectively) in detecting SIBO. Histologic examination of duodenal biopsy specimens did not reveal abnormalities (26/41 dogs), or revealed mild to moderate lymphocytic (12/41) or eosinophilic (2/41) infiltrates, or lymphosarcoma (1/41). Oral antibiotic treatment was effective in 77% (23/30 dogs), but prolonged treatment (> 4 weeks) was required to control signs and prevent recurrence in 50% (15/30). Corticosteroids were used alone in a dog with eosinophilic enteritis and in combination with antibiotics in 4 dogs with marked gastrointestinal lymphocytic/plasmacytic infiltrates. This study suggested that SIBO may be observed in dogs of many breeds, without an obvious primary cause, and that, although results of indirect tests may be suggestive of SIBO, bacterial culture of duodenal juice samples remains necessary for definitive diagnosis.