Abstract: The presently disclosed invention relates to a method of rapid detection and identification of microorganisms including bacteria, viruses, rickettsiae and fungi. The method involves staining all microorganisms or fragments thereof in a sample. The stained sample is introduced onto an optical waveguide coated with a capture molecule specific for the microorganism of interest, and the bound microorganism or fragment thereof is then optically detected. For example, detection of B. anthracis and Salmonella was achieved in times of approximately one minute. The sensitivity of this method is on the order of about 3 cells/.mu.l.