This invention provides novel methods for detecting microorganisms is biological samples. The methods utilize in situ hybridization techniques. In one preferred embodiment, the methods involve blocking binding of nucleic acid probe(s) to granulocytes. The method typically involves contacting a biological sample with a nucleic acid probe that specifically hybridizes under stringent conditions to a nucleic acid of a microorganism and a blocking reagent that is a non-coding nucleic acid, washing the biological sample to remove probe that is not hybridized to a nucleic acid of the microorganism, and detecting the probe where the presence of remaining probe indicates the presence of the microorganism.