Genotyping of cytomegalovirus (CMV) is useful to examine potential differences in the pathogenicity of strains and to demonstrate coinfection with multiple strains involved in CMV disease in adults and congenitally infected newborns. Studies on genotyping of CMV in dried blood spots (DBS) are rare and have been hampered by the small amount of dried blood available. In this study, two multiplex real-time PCR assays for rapid gB and gH genotyping of CMV in DBS were developed. Validation of the assays with 39 CMV-positive plasma samples of transplant recipients and 21 urine specimens of congenitally infected newborns was successful in genotyping 100% of the samples, with gB1 and gB3 being the most prevalent genotypes. Multiple gB and gH genotypes were detected in 36% and 33% of the plasma samples, respectively. One urine sample from a newborn with symptomatic congenital CMV was positive for gB1 and gB2. DBS of congenitally infected newborns (n ؍ 41) were tested using 9 l of dried blood, and genotypes were detected in 81% (gB) and 73% (gH) of the samples, with gB3 being the most prevalent genotype. No clear association of specific genotypes with clinical outcome was observed. In conclusion, the CMV gB and gH PCR assays were found to be rapid, sensitive for detecting mixed infections, and suitable for direct usage on DBS. These assays are efficient tools for genotyping of CMV in DBS of congenitally infected newborns. C ytomegalovirus (CMV) is the most common cause of congenital infection worldwide and an important viral pathogen affecting immunocompromised patients (13, 21). Both in congenitally infected newborns and in immunocompromised patients, genotyping of CMV has been used to study potential differences in pathogenicity of specific strains. However, few authors describe a correlation between specific CMV genotypes and severity of disease (29,32,34,40). More important, genotyping of CMV has enabled the discrimination of reactivation of latent virus from reinfection with new CMV strains in transplant patients, allowing a better definition of donor-to-recipient transmission patterns (24). Congenital CMV infections mainly result from recurrent infections among pregnant women (37), comprising both reactivation and reinfection. The discrimination of reactivation from reinfection may give insight into the mother-to-fetus transmission pattern and the possible associations with the outcome of congenital CMV infections.Genotyping of CMV has mainly focused on envelope glycoproteins gB (UL55) and gH (UL75), which play a role in virus entry and are major targets for neutralizing antibody response. The most frequently used methods for genotyping of CMV are nucleotide sequence analysis (27) and restriction fragment length polymorphism of PCR products (25, 28). Recently, real-time PCR-based assays have been used for rapid detection and quantification of CMV gB and gH genotypes (12,15,24,26). However, they have mainly been applied to plasma or other high-volume samples. Also, deep-sequencing-based methods, sensitive in the de...