Copy number variation (CNV) is common in genomic regions encoding immune-related genes and can impact polygenic autoimmunity. FCGR3B CNV is associated with susceptibility to systemic autoimmunity in Caucasian populations. In this study, we examined FCGR3B CNV in patients with the autoimmune disease lupus nephritis (LN) in a Chinese population. The study includes 202 patients with histologically verified LN and 146 geographically matched healthy controls. To identify CNV at the FCGRB locus, quantitative polymerase chain reaction (PCR) was done with TaqMan( TM) probes and relative copy number was estimated with relative quantitative 2(-DeltaDeltaCt) method. The distribution of FCGR3B relative copy number did not differ significantly between the LN patients and the controls (1.17 +/- 0.42 for LN; 1.15 +/- 0.37 for controls; p = 0.627). The difference was still not significant when the data were stratified by gender. There was no significant difference when the LN patients were divided by pathological phenotype (proliferative LN compared with non-proliferative p = 0.511; AI < 12 compared with AI > or = 12, p = 0.401; and chronicity index (CI) < 4 compared with CI > or = 4, p = 0.058) or lupus disease activity index (SLEDAI < or = 10 compared with SLEDAI > 10, p = 0.996). The data suggest that FCGR3B CNV was not associated with LN development or progression in this Chinese population. These results were surprising given the strong in a Caucasian population.