The treatment of tissue sections to enhance probe access to target mRNA is a critical step in the methodology of in situ hybridization. We have overcome some of the problems encountered in enzyme-based treatment of tissue sections by the application of microwave oven heating. Microwave treatment can (1) replace proteinase K digestion for frozen sections; (2) enhance proteinase K digestion in paraffin sections; (3) denature mRNA structure to enable better probe access; (4) preserve tissue architecture; and (5) inactivate endogenous alkaline phosphatase within tissue sections to reduce background with immunohistochemistry-based probe detection.