Blood infections are one of the major problems of the contemporary medical care. Their detection depends strongly on sensitivity of the used microbiological methods. Widely applied classical techniques based on blood cultivation are time consuming and less sensitive. Therefore, it is necessary to search for new molecular tools to detect bacteria in blood directly taken from patient, like as PCR or FISH. In this paper we have proved that both PCR and FISH show very high sensitivity but due to various limitations their procedures need for further standardization before future application to routine diagnosis of blood infections.