A T-DNA tagged rice population was generated for functional genomic analysis. Using thermal asymmetric interlaced PCR (TAIL-PCR), 159 sequences flanking the right border of T-DNA were obtained. Among them, 92 sequences contained the right border of T-DNA and flanking rice sequences, and 78 flanking rice sequences were mapped as T-DNA tags on 12 rice chromosomes. Integration patterns of T-DNA tags in rice genome were further analyzed using the 78 T-DNA tags and 169 ones reported previously. At junctions of the right border and flanking rice sequences, 14.6% of T-DNA tags (36) showed 3～74 bp of filler sequences. For the T-DNA tags without filler sequences, 21.3% (45) displayed 3～5 bp of microhomology between the nicked T-DNA right border and flanking rice sequences. Filler sequences and microhomology revealed that both double-stranded break and single-stranded gap repair mechanisms played a critical role in the integration of T-DNA into the rice genome. T-DNA integration preferentially occurred in the A/T-rich regions, mainly in the 5′- and 3′-regulatory regions outside the coding regions and in introns of genes.