Mutations of NBS1 are responsible for the human hereditary disease Nijmegen breakage syndrome (NBS), which is characterized by an extremely high cancer rate. In this study, we investigated the influence of NBS1 on ionizing radiation (IR) induced apoptosis. Using small interfering RNA (siRNA) transfection, we knocked down NBS1 protein in three closely related human lymphoblastoid cell lines differing in p53 status: TK6 with a wild-type p53, NH32 with a null mutation of p53, and WTK1 with a mutant p53. We found that up to 48h after 5Gy IR, all three lines showed an obvious induction of apoptosis regardless of the p53 status. The magnitude of apoptosis induction was TK6>NH32>WTK1. This suggested that although p53 is an important modulator of IR-induced apoptosis, other p53-independent apoptosis pathway also exists. Moreover, NBS1 knockdown led to reduction of IR-induced apoptosis in all three lines and both NBS1/ATM/p53/BAX and NBS1/ATM/CHK2/E2F1 apoptosis pathways were partially inactivated. Our results suggest that NBS1 plays an important role in IR-induced apoptosis via both p53-dependent and p53-independent mechanisms. The impaired apoptosis response to DNA damage in NBS1 deficient cells might be one of the important mechanisms of cancer predisposition in NBS patients.