Streptococcus thermophilus, Bifidobacterium infantis Y1 and Bifidobacterium breve Y8 strains were identified and enumerated by PCR assay in human fecal samples after intake of the pharmaceutical preparation VSL-3 or yogurt. ThI/ThII primer set, specific for S. thermophilus, was selected testing its specificity against several strains of enterococci, streptococci and other genera colonizing the human intestine. A culture-independent PCR protocol, developed in this study, allowed to directly detect and enumerate S. thermophilus in human feces, excluding culture-based techniques or time consuming DNA isolation and purification procedures. Intestinal persistence of S. thermophilus was studied in feces of 10 healthy subjects given VSL-3 or yogurt. Streptococcal population was detected after 3 days of administration and persisted for 6 days after the treatment suspension. In the same trial, the colonization kinetics of B. infantis Y1 and B. breve Y8 were studied by amplification of colonies with the strain-specific primer sets InfY-BV.L/R and BreY-BV.R/L, showing a host-dependent transient colonization behaviour. PCR analysis of feces from 10 patients affected by inflammatory bowel diseases (IBD) and treated with VSL-3 for 2 months showed a colonization pattern of S. thermophilus, B. infantis Y1 and B. breve Y8 similar to that observed with the healthy subjects.