The alpha6beta4 integrin is the receptor for the basement membrane protein laminin-5. Recent studies suggest that alpha6beta4 integrin expression in invasive breast carcinomas may be a poor prognostic factor. Because we have not had reliable results with commercially available antibodies for the immunohistochemical detection of alpha6beta4 integrin in archival paraffin-embedded tissues, we designed a probe to detect beta4 integrin subunit mRNA in paraffin sections. In situ hybridization for beta4 mRNA was performed on paraffin-embedded tissue sections of 25 invasive breast carcinomas using a hyperbiotinylated oligonucleotide DNA probe. Immunohistochemical staining was performed on corresponding frozen tumor sections using two commercially available antibodies to the beta4 integrin subunit. All cases positive for beta4 protein by one or both antibodies were also positive for beta4 mRNA by in situ hybridization, but three cases with beta4 mRNA expression were negative by immunohistochemistry with both antibodies. These findings suggest that in situ hybridization appears to be a sensitive method for detecting beta4 integrin mRNA, but it appears to identify some cases that either lack beta4 protein or express variants not recognized with commercial antibodies directed to particular extracellular or cytoplasmic domains.