The submandibular glands were investigated in 77 cases of SIDS using histology, immunohistochemistry (IHC), in situ hybridization (ISH) and PCR to detect cytomegalovirus (CMV) inclusion disease. The aim of the investigation was to establish the detection of CMV by PCR as a model for the detection of other types of virus by PCR, especially for the detection of viruses which affect the respiratory system of babies. In 14 cases the CMV detection was possible. Typical changes of duct cells associated with CMV infection were observed in 9 by histology and in 4 further cases by IHC. In comparison to these methods, ISH showed a higher sensitivity but only one more positive case was found. Theoretically the PCR method is more sensitive than ISH and more convenient from the practical aspect. Detection of CMV by PCR was possible in 10 out of 14 positive cases. All PCR positive cases were cases showing an active disease but not latent infection.