Rice caryopses are enclosed by outer glumes. The size and dimension of the outer glume are the main determinants of caryopsis size. However, it is unclear whether caryopsis development is completely dependent on the size of the glume, or whether it can grow and expand autonomously despite the constraint of glume enclosure. We report the identification of a mutant line that produces normal-sized glumes with smaller mature caryopses that do not fill the entire glume cavity. The caryopsis phenotype in the pex1 mutant is caused by a reduction in cell size. OsPEX1, a leucine-rich repeat extensin gene, was highly expressed in the developing caryopsis. Overexpression of OsPEX1 driven by a constitutive promoter recapitulated the mutant phenotype, showing that the small-caryopsis phenotype is caused by overexpression of the OsPEX1 gene. Free amino acids, including several essential amino acids, and crude protein were increased in pex1 relative to the wild type, endowing pex1 with improved nutritional quality. Our results suggest that caryopsis development can be genetically uncoupled from maternally controlled glume development and that OsPEX1 might be a new resource for improving nutritional quality of rice cultivars.