The diagnosis of bacterial agents of sepsis from blood cultures is crucial for the subsequent treatment of this condition. The aim of this study was to compare Gram stain, culture, and biochemical identification (conventional methods) and fluorescence in-situ hybridisation (FISH) that detects microorganisms from positive blood cultures using specific probes. Another aim was to evaluate the potential of this method for use in clinical practice. Altogether 71 samples of positive blood cultures were tested by FISH. Blood cultures were also processed in the conventional way using the BACTEC analyser. The bacteria recovered were inoculated on solid media and then identified biochemically. The results obtained by the conventional methods and HemoFISH were not 100% concordant. The sensitivity of HemoFISH was 90.1%. Very good results were achieved for staphylococci and enterobacteria. FISH identification failed in three cases because the hybridization probes were not able to bind to bacterial rRNA. The FISH bacterial identification is faster than the conventional methods, but should be confirmed by the latter.