The effects of sd1-d, sd1-r and sd1-c at the sd1 locus, d18-k (kotaketamanishiki dwarf) and d12 (yukara dwarf) on the chilling tolerance at the seedling stage were examined. We used isogenic lines regarding the dwarfing genes/alleles, together with their parental varieties ‘Fujiminori’, ‘Shiokari’, ‘Tamanishiki’, ‘Calrose’, Taichung 65, Norin-PL8 and Norin-PL11. Chilling treatments at 2°C for three, four and five days were conducted at the 1- and 2-leaf stages. The chilling tolerances of the lines were evaluated by survival percentages after the treatments. The d12 lowered the chilling tolerance. The sd1-d and sd1-c lowered the chilling tolerance on the less tolerant genetic backgrounds of ‘Fujiminori’ and ‘Shiokari’, whereas this effect did not appear on the more tolerant genetic backgrounds of Taichung 65 and ‘Calrose’. The d18-k enhanced the chilling tolerance on the less tolerant genetic backgrounds of ‘Shiokari’ and ‘Tamanishiki’, whereas the effect did not appear on the more tolerant genetic backgrounds of Norin-PL8 and Norin-PL11. Consequently, d18-k could be utilized to develop varieties adaptable to areas readily damaged by unseasonably low temperatures at all of the susceptible growth stages of rice, because d18-k is known to enhance the cool tolerances at both the booting and flowering stages also.