The results indicated that the paddy which had a lower moisture content after soaking required a longer incubation time than those which had a higher moisture content. Increasing pre-germination durations caused an increase in α-amylase activities. The rice cultivars and the durations of pre-germination had some effects on changes in the starch yields, chemical compositions, physicochemical properties, and fine structures of isolated PGBR starches. Pre-germination led to lower starch yields of three rice starches and the reduction of AACs of low and high amylose rice cultivars. The starch degradation due to activated α-amylase during pre-germination was also observed through changes in the amylopectin and amylose contents. An increase of the amylopectin content and decrease of the amylose content were observed after pre-germination of KDML105 and RD31. However, the amylopectin and amylose contents of RD6 remained constant during pre-germination. Significant changes in amylopectin branch chain length distributions were found especially for the A chains amylopectin of RD6. A decrease in A chains and increase in B3 chains were found after pre-germination of the three rice cultivars resulting in an increase in pasting temperatures and peak viscosities for the PGBR starches. Therefore, pre-germination could be used as a bio-modification method for modifying rice starches. Some of the quality characteristics of PGBR from the three rice cultivars can be controlled by pre-germination duration and the PGBR can be used as a raw material for specific foods