Sequencing of the entire rice genome has made remarkable progress (IRGSP 2005). This sequence information has provided new tools for genetics and has created a new paradigm of plant breeding. Many phenotypic traits of economic interest are controlled by multiple genes and often show complex and quantitative inheritance. Recent progress in rice genomics has had a great impact on the genetic dissection of such traits into single genetic factors, or quantitative trait loci (QTLs) (Tanksley 1993; Yano and Sasaki 1997). Such genetic factors can subsequently be identified at the molecular level by map-based strategies (Yano 2001). Many QTL mapping studies in rice have been conducted during the last decade. Information on individual QTLs is collected and summarized in a cereal genome database, Gramene (http://www.gramene.org/Oryza_sativa/). It is difficult to review all progress due to the tremendous amount of QTL information in this database. Thus, in this chapter, we summarize QTLs with relatively large effects of economic or agronomic interest. Some of them have already been cloned at the molecular level (Table 1). In addition, we describe the platform for use in the systematic exploitation of natural variations and QTLs and in further analyses of QTLs, such as molecular cloning and marker assisted selection (MAS) for the biological study and breeding of rice.