Alterations in gut microbiota composition offer insights that may be relevant for several chronic conditions, including obesity. This study aimed to evaluate the effect of (−)-epigallocatechin gallate (EGCG) on the modulation of gut microbiota and biomarkers of colonic fermentation end-products in rats. Rats were fed an assigned diet of either a control diet, a 0.3% (w/w) EGCG diet, or a 0.6% (w/w) EGCG diet for 4 wk. Compared to the control group, the addition of 0.6% EGCG to the diet brought about a significant increase in the starch and protein contents in the feces collected in the fourth week of feeding, but the relative weights of abdominal adipose tissues of rats were inversely suppressed. Host-specific bacterial community composition, as determined by terminal restriction fragment length polymorphism (T-RFLP) patterns for fecal 16S ribosomal RNA, showed a significant response in the reduced occupation of Clostridium spp. and an increased trend of Bacteroides by dietary supplementation with EGCG. The 0.6% EGCG diet also influenced the status of Bifidobacterium and Prevotella to a lesser extent. Interestingly, the cecum of rats fed the 0.6% EGCG diet contained lower levels of acetic and butyric acids, whereas EGCG had little influence on the cecal level of propionic acid. EGCG also reduced the cecal p-cresol concentration in a dose-dependent fashion. In conclusion, dietary EGCG affects the growth of certain species of gut microbiota in rats and is associated with the cecal pattern of short chain fatty acids which could be responsible for regulating energy metabolism in the body.