The intestinal microbiota represents the largest and the most complex microbial community inhabiting the human body. Bifidobacteria and lactobacilli represent important commensal bacteria with the ability to utilize complex carbohydrates. The main fermentation products from the breakdown of complex dietary carbohydrates are short chain fatty acids (SCFAs). We examined faecal samples of vegetarians (n = 10) and conventional omnivores (n = 10) to evaluate the counts and occurrence of cultivable bacteria, especially bifidobacteria and lactobacilli, using cultivation on selective media, and matrix-assisted laser desorption/ionization time-of-flight. Moreover, concentrations and molar proportion of SCFAs in faecal samples were measured. Total counts of Gram-negative anaerobic bacteria were significantly lower (P < 0.05) in vegetarian faecal samples, while others (total anaerobic bacteria, Bifidobacterium spp., Lactobacillus spp., Escherichia coli, and presumptive coliforms) were not. Neither total concentrations nor molar proportions of SCFAs in faecal samples differed (P > 0.05) between the diet groups. In total, six Bifidobacterium spp. and thirteen Lactobacillus spp. were detected via culture-dependent methods. Bifidobacteria counts and species composition in faecal samples of both groups were found to be relatively similar, regardless of the diet. Lactobacillus species varied more by individual diet.