The transfer of the long T-DNA (T-DNA and non-T-DNA) of a binary plasmid from Agrobacterium into the rice genome was investigated at both molecular and genetic levels. Out of 226 independent transgenic plants, 33% of the transformants contained non-T-DNA sequences. There was no major difference in the frequency of non-T-DNA transfer among three Agrobacterium tumefaciens strains. Four T1 plants containing a single putative long T-DNA insertion were selected for Southern analysis. Three of them were confirmed to have a long T-DNA insertion with a size of greater-than-unit-length of the binary plasmid. This was further confirmed by rescuing the intact binary plasmid from these plants. Our results suggest that long T-DNA transfer by rolling-circle replication from Agrobacterium to rice occurs frequently, and that the high frequency of non-T-DNA transfer should be considered when producing transgenic rice for commercial production.