Background: Accumulated evidence has shown that hepatitis B virus infection is associated with numerous types of nephropathy but it remains to clarify the different role of HBV markers, either in serum or deposit in kidney, in the pathogenesis of HBV-associated nephropathy. In this study, we investigated the relationship between HBV markers and HBV-associated nephropathy by using multi-linear regression in Chinese patients with HBV-associated membranous nephropathy (MN). Methods: A total of 196 cases of HBV-associated MN, which were diagnosed based on renal biopsy, were collected during the period of January 2000 to December 2009 from our hospital. Serum and renal biopsy HBV markers included HBsAg, anti-HBs, HBeAg, anti-HBe, and anti-HBC. HBV-associated nephropathy was characterized by a panel of clinical manifestations and pathological parameters, which included proteinuria, hematuria, serum creatinine, hypertension, and renal damage in glomeruli, tubules, interstitium, and blood vessels. Multilinear regression was used to analyze the relationship between the HBV markers in serum and renal biopsy and the clinicopathological characteristics of HBV-associated nephropathy. Results: After analysis of the clinical and pathological data in 196 cases of HBV-associated membranous nephropathy, this study revealed that glomerular lesion was marginally associated with serum HBsAg (P = 0.0528), Anti-HBs (P = 0.0978), but significantly associated with the presence of IgA (P = 0.0242), IgG (P < 0.0001) and C3 (P = 0.0064) in renal biopsy. There was no significant association between glomerular lesion and HBV markers in kidney. The presence of crescent and renal tube impairment was not related to HBV markers. The renal fibrosis was significantly related to gender (P = 0.023), age (P = 0.0211), HBsAg (P = 0.0001) and HBcAg (P = 0.0083) and C3 (P = 0.0299) in renal biopsy. Notably, the renal blood vessel impairment was significantly related to systolic Blood Pressure (SBP) (P < 0.0001), diastolic blood pressure (DBP) (P = 0.0002), serum HBsAg (P = 0.0428), serum HBeAg (P = 0.0766), FRA (P = 0.0002), and HBsAg (P = 0.0241) and HBcAg (P = 0.0599) in renal tissues. Also, the renal interstitial infiltration was related to patient age (P = 0.015, SBP (P < 0.0001), DBP (P = 0.0001), C3 (P = 0.0028), FRA (P = 0.0165), HBsAg (P = 0.0016) and HBcAg (P = 0.0203) in kidney biopsy. These results suggest that the major pathological changes in kidneys in HBV patients are related to one or more HBV markers, such as HBsAg, HBeAg, or anti-HBs antibody. Besides, most of the pathological changes in kidneys are related to C3 and FRA in kidney tissues. The clinical markers of nephropathy, such as proteinuria, hematuria and creatine serum levels, were also evaluated for their relationship with HBV markers in serum and kidney tissues. We found proteinuria was marginally related to HBV DNA (P = 0.0537), significantly related to IgA (0.0223). Hematouria was significantly related to IgA (P = 0.0434), IgG (P < 0.0001), and C1q (P = 0.0282). The serum creatine level was related to patient gender (P = 0.0077), SBP (P < 0.0001), DBP (0.0049), IgG (P-0.0006), and C3 (P = 0.0113). These clinical manifestations were not related to HBV markers in either serum or kidney. These results indicate that some of clinical manifestations of nephropathy are related to HBV markers, but the relationship is limited.