Although F2s are the most informative populations for genetic analysis, it has been difficult to use F2 populations directly for QTL analysis because it is usually difficult to assess the reliability of the data, due to an inability to estimate the experimental errors. In this study, we performed a QTL analysis for yield and yield-component traits of an F2 population based on data from replicated field trials over 2 years using vegetative shoots of ratooned plants, making use of the ratooning habit of rice. The objective of this study was to explore the possibility of conducting QTL analyses directly based on an F2 population by means of ratooning plants. The experimental population was from a cross between ’Zhenshan 97’ and ’Minghui 63’, the parents of ’Shanyou 63’, an elite rice hybrid widely grown in China. A genetic linkage map containing 151 molecular markers was constructed for QTL mapping. A total of 20 distinct QTLs were detected; eight of these were detected in both years and remaining 12 in only 1 year. Compared with the results of our previous analysis of the F2:3 families from the same cross, it was shown that most of the QTLs detected in the ratooned F2 population were also detected in the F2:3 population. However, the estimates of both additive and dominant types of genetic effects for many of the QTLs based on F2 ratoons were substantially larger than those based on F2:3 families. The results indicate that vegetatively ratooned F2 populations may have considerable utility in the mapping of QTLs, especially if dominant types of gene actions are of concern, although there were certain technical limitations in making use of such populations in the experiments.