The genotypic differences of callus cultures derived from selected rice varieties belonging to three subspecies namely Indica, Japonica and Javanica were evaluated based on their morphology and ultrastructures. Genotypic differences were observed in the morphology as well as in the ultrastructures of the selected varieties under each subspecies. Based on morphology, two types of calli were observed two weeks after culture in the Indica varieties: one was light yellow, compact, smooth-surfaced and the other was yellowish with hair-like projections and tiny green spots. The calli of the Japonica and Javanica varieties were yellowish, compact and had smooth surface. Four weeks after culture, progression of the green spots was noted in the Indica variety, IR 54. Calli of the Japonica varieties remained compact and smooth while that of the Javanica variety became granular in appearance. Histological observation of the resin sections of the calli in all varieties showed darkly stained meristematic cells. The meristematic T cells in Indica variety, IR 54, were found in the inner portion of the callus mass while that in the Japonica varieties were observed in the peripheral area of the callus mass. The meristematic cells in Javanica variety, Rinatte, were scattered all over the callus mass. Scanning electron microscopy revealed distinct differences in the ulrastructures of the callus derived from the different varieties studied. Calli of Indica variety had compact cell mass with dome-like structures while callus in the Japonica and Javanica varieties had compact, globular cell masses.