Real-time polymerase chain reaction (PCR) and nested reverse transcription (RT) PCR were applied to demonstrate the viability of lactobacilli in the feces of volunteers fed fermented milk containing lactobacilli. Two sets of specific primers and a TaqMan probe for real-time PCR were constructed using the S-layer gene as a target. After fermented milk ingestion, Lactobacillus helveticus GCL1001 was detected in the feces of 12 volunteers over a few days, with the maximum number being between 10(4.5) and 10(7.8) cells g(-1) of feces. Moreover, mRNA from this strain was detected in the feces of all volunteers by nested RT-PCR. The results show that these methods are applicable to the demonstration of bacterial viability in feces, and that ingested L. helveticus GCL1001 can survive through the gastrointestinal tract.