Human cytomegalovirus (HCMV) infection is an important cause of neonatal death. Using primers derived from sequences within the morphological transforming region II (mtrII), HCMV DNA was amplified by polymerase chain reaction (PCR) from fixed tissues of infants who had died of congenital HCMV infection. In one neonate, HCMV DNA with reduction in the expected size was detected in the liver, spleen, kidney, adrenal, und thyroid tissues by gel electrophoresis. Nucleotide sequencing of the PCR product revealed a 65bp frame-shift deletion within the 79 amino acid open reading frame (ORF) of the mtrII. Based upon this observation, it is likely that viral genomic rearrangement involving the mtrII may occur in some cases of congenital HCMV infection.