The distribution and clearance of viral RNA (vRNA) and mRNA has been analysed for the acute and recovery stages of the pneumonia induced by intranasal infection of C57BL/6J mice with H3N2 influenza A viruses. Amplification of viral genomic material by the polymerase chain reaction showed that the influenza haemagglutinin (HA) gene was eliminated from the lungs of immunologically intact mice by day 14 post-infection, whereas in vitro depletion of the CD4+ T cells delayed clearance by at most 4 days. Viral RNA encoding the HA gene was first demonstrated in the regional mediastinal lymph nodes at 48 h, and continued to be present until day 6 or day 10 after infection of the intact and CD4-depleted mice, respectively. Evidence for the presence of vRNA in the thymus, but not in the mesenteric lymph nodes or the spleen, was found in some situations. Otherwise, the distribution and clearance of vRNA was as would be predicted from earlier studies using virus isolation procedures to monitor localization patterns, and shows a lack of long-term persistence of the influenza virus genome.