Objectives: To explore the capacity of mutant lactobacilli to remove creatinine (Cr) and urea nitrogen (UN) via the gastrointestinal tract and its effects on renal pathology in the 5/6 nephrectomized rat model of chronic renal failure.Methods: Sixty Sprague–Dawley rats were randomly divided into a Sham group, a Model group, a wide-type Lactobacilli group (L.B group), and a Mutant Lactobacilli group (Mut-L.B group). The rats in the Model, LB and Mut-L.B groups underwent 5/6 nephrectomy. Eight weeks after administration, 24-h urine, orbital blood and digestive secretions were collected to analyze Cr and UN levels. Pathological changes in nephridial tissues were observed by hematoxylin and eosin and Masson trichrome staining, and the expression of TGF-β1 and FN was detected by immunohistochemistry.Results: There were no significant differences in urinary Cr and UN levels among the Sham, L.B and Mut-L.B groups (p > .05), while serum and digestive Cr and UN levels were significantly decreased in the Mut-L.B group (p < .01). Furthermore, renal tubular injury and interstitial fibrosis were significantly reduced and TGF-β1 and FN expression was decreased (p < .05) in the Mut-L.B group.Conclusion: Mutant lactobacilli decreased serum Cr and UN levels, reduced the expression of TGF-β1 and FN in renal tissues and alleviated renal interstitial injury and fibrosis in a rat model of chronic renal failure in a mechanism that may involve decomposition and not just excretion of small molecule toxins in the gastrointestinal tract.