Acute inflammatory processes are extremely complex, containing sets of activated cells that may be difficult to categorize. The interface between two methodologies for characterizing the involvement of γδ T cells, in situ hybridization to detect T cell receptor (TCR) mRNA and flow cytometric analysis of surface TCR expression, is utilized here to study the pneumonia caused by intranasal (i.n.) infection of mice with influenza A viruses. Substantial numbers of cells expressing mRNA for the γ and δ TCR chains are present in bronchoalveolar lavage (BAL) populations obtained either late in the course of primary infection with an H3N2 virus or within a few days of secondary challenge with an H1N1 virus. The majority of the γδ TCR mRNA+ cells detected in FACS-separated BAL populations partition to the Thy1+ γδ TCR+ subset, while relatively few (<10%) Cδ mRNA transcripts are found in cells that phagocytose latex particles. However, an additional set of γδ TCR mRNA+ cells is also located in a high side scatter (H-SSC) population, which stains nonspecifically with monoclonal antibodies (mAbs) and is normally gated out in the process of flow cytometric analysis. This H-SSC population tends to be enriched for cells expressing Cγ 1 2 rather than Cγ4 mRNA. While some γδ TCR lymphocytes can be demonstrated by in vitro stimulation of the CD3ε{lunate}+ subset within this H-SSC population, the majority of the γδ T cell precursors that can be expanded in culture demonstrate a low side scatter (L-SSC) profile more characteristic of normal T lymphocytes. The possibility that subsets of activated, granular (H-SSC) αβ TCR+ and Cγ 1 2 mRNA+ γδ T cells are being missed when conventional FACS analysis is used to study this viral pneumonia is discussed. © 1992.