Only two genome-wide association studies (GWAS) have been conducted to date to identify potential markers for total mortality after diagnosis of breast cancer. Here we report the identification of two SNPs associated with total mortality from a two-stage GWAS conducted among 6,110 Shanghai-resident Chinese women with TNM stage I-IV breast cancer. The discovery stage included 1,950 patients and evaluated 613,031 common SNPs. The top 49 associations were evaluated in an independent replication stage of 4,160 Shanghai breast cancer patients. A consistent and highly significant association with total mortality was documented for SNPs rs3784099 and rs9934948. SNP rs3784099, located in the RAD51L1 gene, was associated with total morality in both the discovery stage (P=1.44×10−8) and replication stage (P=0.06; P-combined=1.17×10−7). Adjusted hazard ratios (HR) for total mortality were 1.41 (95%CI=1.18–1.68) for the AG genotype and 2.64 (95%CI=1.74–4.03) for the AA genotype, when compared with the GG genotype. The variant C allele of rs9934948, located on chromosome 16, was associated with a similarly elevated risk of total mortality (P-combined: 5.75×10−6). We also observed this association among 1,145 breast cancer patients of European-ancestry from the Nurses’ Health Study (NHS; P=0.006); the association was highly significant in a combined analysis of NHS and Chinese data (P=1.39×10−7). Similar associations were observed for these two SNPs with breast cancer-specific mortality. This study provides strong evidence suggesting that the RAD51L1 gene and a chromosome 16 locus influence breast cancer prognosis.