The polymerase chain reaction (PCR) was used in combination with microbiology methods for identifying faecal bacteria. The changes were monitor in the bacterial flora of chicken’s caecum after preventive peroral application of Enterococcus faecium EK13 and consecutive infection with Salmonella enterica subsp. Enteritidis.The preventive treatment with Enteroccocus faecium EK13, reduced the numbers of S. enterica subsp. Enteritidis in chicken excreta after 5 days post infection (pi) and in the caecum after 7 days pi. The PCR products 243 bp for Sallmonella spp. and 550 bp for Ent. faecium were amplified. The detection of Salmonella spp. required only simple boiling of the samples. On the contrary, for reliable detection of Ent. faecium, DNA isolation with commercial available kit was required. The high sensitivity of PCR was confirmed and the expected specific DNA fragments could be amplified from dilutions containing ten to one CFU (Colony Forming Units).