Low bone mineral density (BMD) is suggested to be associated with increased mortality in the general health population, but the relationship in chronic kidney disease (CKD) patients is still unclear. We performed a meta-analysis to investigate the association of BMD in different sites with risk of all-cause mortality in CKD patients. We searched PubMed, EMBASE, and Web of Science to identify eligible cohort studies that evaluated the association between BMD at different sites and risk of all-cause mortality in CKD patients. Twelve cohort studies were identified, which included 2828 CKD patients and 1052 deaths. Compared with normal/high level of total body BMD, lower total body BMD was associated with 25% higher risk of all-cause mortality. The pooled relative risk (RR) was 1.25 (95% confidence interval [CI] 1.09, 1.42) with little heterogeneity across studies. Regarding BMD measured at different sites, the risk of all-cause mortality was highest for lower BMD at hip/femoral neck (pooled RR = 1.69;​ 95% CI 1.20, 2.40). The pooled RRs were 1.26 (95% CI 1.04, 1.53) and 1.17 (95% CI 1.00, 1.37) for lower BMD at arm and spine, respectively. Similarly, the risk of death for per SD decrease in BMD was also higher at hip/femoral neck (pooled RR = 1.43, 95% CI 1.15, 1.77) compared with arm (pooled RR = 1.03, 95% CI 1.00, 1.06) and spine (pooled RR = 1.17, 95% CI 0.98, 1.39). In conclusion, lower BMD values at hip, arm, spine, as well as the whole body are associated with increased risk of all-cause mortality in CKD patients. The excess risk is highest for patients with lower BMD at hip/femoral neck, suggesting BMD measured at hip region may be the best indicator of mortality risk in CKD patients.