Background Human cytomegalovirus (HCMV) infects a number of organs and tissues in vivo. The different symptoms and tissue tropisms of HCMV infection perhaps result from genetic polymorphism. A new region of DNA containing at least 19 open reading frames(ORFs) (denoted UL133 to 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. One of these genes, UL143, was studied to explore the sequence variability of UL143 ORF in HCMV clinical isolates and examine the possible association between gene variability and the outcome of HCMV infection. Methods The UL143 gene of the strains obtained from suspected congenitally HCMV-infected infants was amplified by polymerase chain reaction (PCR) and sequenced. Results Nineteen sequences of the strains were divided into 2 major groups, G1(n=16) and G2(n=3). All of the sequences had frame-shift mutation compared to Toledo. Nucleotide polymorphisms conferred substantial amino acid substitutions when compared with Toledo. All 16 UL143 putative proteins of the strains in G1 had a new myristylation site and loss of two PKC sites owing to missense mutations. No convincing relationships were observed between the presence of HCMV disease and the UL143 sequence group. Conclusions HCMV-UL143 existed in low passage isolates. Sequence variability caused by frame-shift mutation was found in all HCMV clinical strains. No obvious linkage was observed between UL143 polymorphisms and the outcome of suspected congenital HCMV infection. Background Human cytomegalovirus (HCMV) infects a number of organs and tissues in vivo. The different symptoms and tissue tropisms of HCMV infection may result from genetic polymorphism. A new region of DNA containing at least 19 open reading frames (ORFs) 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. One of these genes, UL 143, was studied to explore the sequence variability of Methods The UL143 gene of the strain obtained from attempted HCMV infection isolates and examine the possible association between gene variability and the outcome of HCMV infection. Methods The UL143 gene of the strain obtained from suspended congenitally HCMV-infected infants was amplified by polymerase chain reaction (PCR) and sequenced. Results Nineteen Sequences of the strains were divided into 2 major groups, G1 (n = 16) and G2 (n = 3). All of the sequences had frame-shift mutation compared to Toledo. Nucleotide polymorp all 16 UL143 putative proteins of the G1 in a new myristylation site and loss of two PKC sites due to missense mutations. No convincing relationships were observed between the presence of the HCMV disease and the UL143 sequence group. Conclusions HCMV-UL143 existed in low passage isolates. Sequence variability caused by frame-shift mutation was found in all HCMV clinical strains. No obvious linkage was observed between UL143 polymorphisms and the outcome of suspected congenital HCMV infection.