Abstract The objective of this work was to determine the genetic correlations and the direct and indirect associations of agronomic traits and grain quality attributes with the percentage of whole grains in flood irrigated rice. The experiment was carried out in two environments, in a randomized complete block design with three replicates, using 23 irrigated rice genotypes. The evaluated traits were: percentage of whole grains, caryopsis length, caryopsis width, panicle length, panicle weight, 1,000 grain weight, days to flowering, percentage of chalky grains with white belly, total chalky area, total whiteness, vitreous whiteness, and defects in coloring. The percentage of grains with white belly and total chalky area were positively correlated, whereas the percentage of grains with white belly and vitreous whiteness were negatively correlated. The traits caryopsis width, percentage of chalky grains with white belly, panicle weight, and 1,000 grain weight showed indirect effects on whole-grain yield response according to total chalky area and total whiteness. Total chalky area and total whiteness are the factors that most negatively influence the percentage of whole grains according to the genotypic correlations and direct effects.