To investigate the epidemiological pattern of Borna disease virus (BDV) infection in horses and to analyze the phylogenetic tree of derived BDV in Yili, Xinjiang.We established a modified nested RT-PCR (nRT-PCR) to detect BDV p24 segment in peripheral blood mononuclear cells (PBMCs) and brain tissues of 120 horses in Yili, Xinjiang. Positive products were analyzed by sequencing and homology analysis.The positive rate of BDV infection was 2.5% in both PMBCs and brain tissues at the same time. The gene sequence revealed in positive PCR samples was more than 93%, identical to that of BDV derived from horses in other countries. We also noticed a high degree of identity (> 98%) to standard strain He/80 in gene sequence of positive PCR samples.Our study found the presence of BDV natural infection in horses in Yili. The endemic BDV had a high degree of identity to standard strain He/80.