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The aim of the present study was to identify the virulence of glycoprotein B (gB), glycoprotein N (gN), and glycoprotein H (gH) genotypes of cytomegalovirus(CMV) and assess possible relationships between genotypes and CMV-associated thrombocytopenia. CMV gB, gN, and gH strains were determined by nested PCR and restriction length polymorphism from 30 CMV-associated thrombocytopenia infants infected postnatally and 40 non-thrombocytopenic infants. The gN2 (p = 0.043) and gH2 (p = 0.038) genotypes were associated with an elevated risk of developing thrombocytopenia. gB1 genotype was detected in 80.0% (16/20) of infants with moderately to severely symptomatic CMV disease and was associated with severe manifestations in CMV-associated thrombocytopenia infants (p = 0.022). Conversely, the gN1 genotype was detected in 5.0% (1/20) of infants with moderately to severely symptomatic CMV disease and represent less pathogenic CMV strains (p = 0.044). There may be potential associations between the gN2 and gH2 genotypes of CMV and infantile thrombocytopenia, and that the detection of the gB1and gN1 genotypes may help define the severity of CMV disease in infants.