The aim of this study was to evaluate the effect of probiotic oligosaccharides (POS) on the recovery of bowel atrophy induced by protein malnutrition (PM) in rats. Thirty male Wistar rats (200 to 250 g) were fed with a conventional diet for 10 days of adaptation. After this period, the rats are divided into 3 groups. A control group was fed with a conventional diet (n = 10), and a group of 20 rats was subjected to PM for 15 days. After period of PM, 10 rats were refed with enriched POS diet for 10 days (Lactobacillus acidophilus, Lactobacillus rhamnosus, Bifidobacterium lactis, Bifidobacterium longum, Bifidobacterium bifidum, Streptococcus thermophilus and fructo-oligosaccharides at 0.5 mg/g body weight/day). Our experimental protocol was developed to evaluate some nutritional biochemical parameters such as total proteins, globulin and albumin and morphometric parameters of the intestine. Biochemical parameters caused a significant decrease in the concentration of total protein, albumin and globulin in malnourished rats as compared between the control and group rats. These biochemical values increased in rats refed with POS. The data obtained in the study suggest that PM causes alterations in rat colon and small intestinal morphometry, especially in tissues which present a high level of cell turnover such as the mucosa tunic and consequently their structures such as the enterocytes, goblet cells and crypts. Probiotics oligosaccharides enhanced the recovery of gut atrophy induced by protein malnutrition. Probiotic oligosaccharides can be useful as oral adjuvant during the recovery of protein malnutrition.