Objectives: Human cytomegalovirus (HCMV) infects a number of organs and cell types in vivo. The different symptoms and tissue tropisms of HCMV infection perhaps result from the genetic polymorphism. A new region of DNA containing at least 19 open reading frames (ORFs – denoted UL133–151) was found in the low-passage HCMV clinical strain Toledo and several other low-passage clinical isolates, but not present in the HCMV laboratory strain AD169. Two of these genes, UL146 and UL147, encode proteins with sequence characteristics of CXC (α) chemokines, suggesting that they might influence the behavior of neutrophils during infection. This research was to study the sequence variability of UL146 and UL147 ORFs in HCMV clinical isolates and examine the possible associations between gene variability and the outcome of HCMV infection. Methods: UL146 and UL147 genes from strains obtained from suspected congenitally HCMV-infected infants were PCR amplified and sequenced. Results: High variability was found in UL146 and UL147 gene among HCMV clinical strains. However, the α chemokine motif in UL146 and UL147 genes was conserved in almost all sequences. According to the phylogenetic analysis, all sequences of UL146 in clinical isolates could be divided into three groups. All strains from congenital megacolon infants existed in G2A only, and all from asymptomatic infants existed in G2B peculiarly. Conclusions: Sequence variability among HCMV clinical strains may affect the ability of UL146 and UL147 to attract human neutrophils and influence viral dissemination. No obvious linkage was observed between UL146 polymorphisms and outcome of suspected congenital HCMV infection.