Nested polymerase chain reaction (PCR) amplifying the morphological transforming region II (mtrII) of cytomegalovirus (CMV) has been shown to be useful in the detection of CMV DNA in bone marrow transplant (BMT) recipients. However, there has never been any report on mutation hot spots and subtypes of this open reading frame. Using primers derived from sequences upstream and downstream of mtrII (ORF 79), CMV DNA from peripheral blood leukocytes (PBL) and conventional CMV culture of 16 BMT recipients were amplified by PCR, cloned into pUC118, and sequenced. The amino acid sequences were predicted using the standard triplet code. The DNA sequences obtained from direct amplification of CMV in PBL obtained from the 16 patients were 100% identical to the corresponding ones obtained by amplification of CMV DNA extracted from conventional CMV culture. Within mtrII (ORF 79), hot spot single base mutations were observed at positions +40 (G-->A), +123 (A-->G), +213 (T-->C), and +219 (T-->C). However, because of third base degeneracy, only amino acid 14 was changed from valine to isoleucine in the predicted protein of 13 patients. This corresponded to the hot spot mutation at position +40 (GTC-->ATC), while the rest were silent mutations. An insertion of 3 bases (ACG) was observed in the CMV DNA of 10 patients at positions +91 to +93, leading to a threonine insertion at amino acid 31 in these patients. For patient no. 147 there was a 65 bp deletion in the CMV DNA amplified later in the course of BMT as compared with that early in the course. This gave rise to a frame shift mutation and a change of more than 70% in the predicted amino acid sequence of the protein.