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It was reported that probiotics could maintain the balance of intestinal microfloral and increase intestinal immune system. The objective of this study was to analyze the influence of indigenous probiotic Lactobacillus fermentum and Lactobacillus plantarum on the morphological profile of small intestine of Enteropathogenic E. coli (EPEC)- infected rats. This study was done from August to November 2011 at Bogor Agricultural University. A total of 90 male rats Sprague Dawley were used in this study. They were devided into 6 groups; negative control (A), Lactobacillus plantarum treated (B), Lactobacillus fermentum treated (C), Lactobacillus plantarum and EPEC treated (D), Lactobacillus fermentum and EPEC treated (E), and EPEC infected group (F). The treatments were done for 21 days. Small intestine tissues were processed using paraffin embedding standard method and stained with haematoxylin eosin. The data were analyzed using analysis of variance (ANOVA). The results showed that L. fermentum and L. plantarum treatments decreased percentage of small intenstine villi damage (14 to 62%) and increased the thickness of small intestine mucosa (14 to 29%). In conclusions, treatment of indigenous probiotic L. fermentum and L. plantarum increase the health of small intestine. L. fermentum give better effect in inhibiting the damage of small intestine of rats, which under EPEC infection.