The objective of this study was to characterize the main-effect QTLs, epistatic QTLs and QTL-by-environment interactions (QE), which are involved in the control of protein content. A population of 120 doubled haploid (DH) lines derived from a cross between 'Samgang' and 'Nagdong', was planted and determined for protein content over three years. Based on the population and a genetic linkage map of 172 markers, QTL analysis was conducted by WinQTLcart 2.5 and QTLMAPPER. Three main-effect QTLs affecting protein content of brown rice were detected from 2004 to 2006 on chromosomes 1 and 11. The qPC11.2 was repeatedly detected across two years. Seven pairs of epistatic loci were identified on eight chromosomes for protein content and collectively explained 39.15% of phenotype variation. These results suggest that epistatic effects might be an even more important component of the genetic basis for protein content and that the segregation of the DH lines for protein content could be largely explained by a few main-effect QTLs and many epistatic loci.