A t (11; 22)(q24; q12) translocation is present in 90% of Ewing's sarcoma, and results in the formation of the EWS-FLI1 fusion gene encoding an oncogenic transcription factor. To clarify the function of chimeric EWS-FLI1 proteins, an identification of a nuclear localization signal (NLS) in the EWS, FLI1 and EWS-FLI1 proteins is important because the chimeric oncoprotein may lose or gain NLS function different from native proteins resulting in different subcellular localization, and in deregulated gene expression. Furthermore, some studies reported that patients with one type of fusion gene (‘type 1’) had better overall survival than those with other types, suggesting that functional differences may be present among various fusion proteins. There has been only one study reporting a NLS in EWS, but none reporting those in FLI1 and EWS-FLI1. To clarify the molecular mechanisms of Ewing tumor development, we first identified the NLSs of EWS and FLI1. We allocated the NLS to amino acid residues 632-656 near the C-terminal region of EWS that is different from the previous study, and identified two NLSs of FLI1, NLS1 (63-90) in the N-terminal domain and NLS2 (319-360) in the 3'-ETS domain. In addition, the present study showed that all of the EWS-FLI1 fusion proteins completely reside in the nucleus without affecting the frequency of nuclear localization among variants, suggesting that NLS2 of FLI1 was used for nuclear translocation of various EWS-FLI1 fusion proteins.