The 2004 Mid Niigata Prefecture earthquake (37.289 degrees N, 138.870 degrees E, 13.1 km, M-JMA 6.8; JMA), also known as the 2004 Niigata Prefecture Chuetsu earthquake, was a thrust type earthquake that occurred on October 23, 2004 at 17:56 (JST). Strong ground motions of PGA 800-1700 cm/s(2) and PGV 60-130 cm/s were observed at stations located immediately above the source region. We deduced the rupture process of this earthquake with a multi-time-window linear waveform inversion procedure. We used near-fault strong ground motion data observed at nine K-NET and KiK-net stations within 50 km from the epicenter. In order to obtain appropriate Green's functions for the waveform inversion, we constructed two velocity structure models for stations on the hanging wall and one structure model for stations on the footwall. The estimated total slip distribution contains three asperities: (a) around the hypocenter, (b) in the upper-middle section of the fault plane, and (c) southwest of the hypocenter. The maximum slip is 3.8 m at the hypocenter and the total seismic moment is 1.2 x 10(19) Nm, which corresponds to M omega=6.7. The moment rate functions in asperities (a) and (c) have a short rise time, while those in asperity (b) have a longer rise time.