Distribution of indigenous lactobacilli in the gastrointestinal tracts of rats was investigated at the species level. The indigenous lactobacilli isolated from conventional rats were divided into three groups, Lactobacillus acidophilus and its related strains, L. fermentum, and L. murini. Localization of the Lactobacillus groups in the gastrointestinal tracts could be distinguished clearly based on arabinose and glucose fermentation reaction of isolates from each part of the gastrointestinal tract. Group I (L. acidophilus and the related strains) and Group II (L. fermentum) were the major populations of lactobacilli on the walls of the non-glandular part and in the contents of the stomachs of both conventional and gnotobiotic rats. Group I predominated in all the parts of the digestive tract of conventional rats, whereas Group II was in the minority in the lower part of the gastrointestinal tracts of both groups of rats. Group III (L. murini) was the predominant population of Lactobacillus in the lower part of small intestine of conventional rats and in all parts of the gastrointestinal tracts of gnotobiotic rats except for the wall of the nonglandular part of the stomach.To understand the complicated interactions between the host and its intestinal microflora, further investigations of such aspects as gastrointestinal location, bacterial species or types, levels of population, mode of colonization, and interactions of intestinal bacteria should first be made.Lactobacilli are considered to be the most important members of the intestinal microflora of mice and rats judging from their mode of colonization, i.e. high population levels (3) and association with mucosal epithelia (1). However, little is known about the indigenous Lactobacillus species, their distribution in different areas of the tracts, the intestinal interrelationships between lactobacilli and other bacteria, etc. We previously demonstrated the localization and population of indigenous bacterial flora at the genus level in the gastrointestinal tracts of conventional and gnotobiotic rats (9). This paper reports the localization and population of indigenous lactobacilli at the species level in various parts of the gastrointestinal tracts of conventional and gnotobiotic rats.