The microorganisms causing nosocomial infections belong either to the patient himself (endogenous infections) or to hospital flora. New epidemiological tools, using molecular technologies, have renewed the body of knowledge on this flora. The commonest pathogens producing nosocomial infections include coagulase positive or negative staphylococci, enterococci, enterobacteriaceae, pseudomonas and candidas. A recent trend has been shown, indicating the emergence of Gram positive cocci and fungi, when E. coli and Klebsiella tend to decrease. Bacterial resistance to antimicrobials is a growing concern, with the appearance of new resistance mechanisms such as extended-septrum betalactamases in Gram negative rods, vancomycin resistance in several Gram positive species, or multiply resistance in enterococci, staphylococci, pseudomonas or mycobacteria. Some pathogens create new concerns nowadays, such as M. tuberculosis, M. avium intracellulare, Gram positive bacilli (exemplified by Corynebacterium JK), water bacteria, non-albicans Candidas and other fungi. Increasing therapeutic challenge underlines the proeminant role of infection control programs.