Most of our understanding of the human colonic microbiota is derived from studying the microbial contents of fecal samples, because it is impractical to access the human large intestine during normal digestion, and as an alternative, bacteria detected in feces are most representative of populations present in distal region of the intestine. The colonic microbiota is suggested to play an important role in protection against pathogens and has important trophic effects on intestinal epithelia and immune structure and function. This chapter discusses methods for monitoring the intestinal microbiota, including culture techniques and molecular-based techniques. An alternative approach to probiotics for intestinal microbiota modulation is the use of prebiotics. The best currently recognized prebiotics in Europe are fructooligosaccharides (FOS), galactooligosaccharides (GOS), and lactulose, which (except for lactulose) are legally classified as food or food ingredients. The majority of clinical trials with humans have focused on demonstrating their efficacy in increasing intestinal levels of bifidobacteria and sometimes lactobacilli in fecal samples of healthy subjects. The most documented and recognized effect of prebiotics is the promotion of the growth of beneficial bacteria in the colon.