Because high temperatures impair rice production, it is desirable to elucidate the regulatory mechanisms involved in rice response to heat stress. The objectives of this study were to identify candidate genes and characterize their response patterns during rice adaptation to high temperatures at the seedling stage. Ten heat-associated quantitative-trait loci were identified in a genome-wide association study. Comparison of transcript abundances in heat-sensitive and heat-tolerant rice pools under heat stress revealed approximately 400 differentially expressed genes. The expression of genes from heat-sensitive accessions changed more than those from heat-tolerant accessions under heat stress. Alternative splicing (AS) events responded to heat stress in rice. The types of AS variants significant different between the heat-sensitive and heat-tolerant accessions. Expression patterns differing between the heat-sensitive and heat-tolerant accessions were identified for genes known to be involved in heat stress. We identified eleven genes associated with rice heat stress response. These genes could be pyramided to breed heat-tolerant rice accessions.