We used nested multiplex polymerase chain reaction to determine the distribution of cytomegalovirus gB genotype in 30 Mexican children undergoing bone marrow transplantation. The genotypes were: gB1, 9/30 (30%); gB2, 8/30 (27%); gB3, 4/30 (13%), and gB4, 1/30 (3%); mixed genotypes were identified in 8/30 patients (27%). We conclude that the predominant genotypes identified were gB2 and gB1. The gB5 genotype was not detected, and a high proportion of mixed genotype was found.