To elucidate changes in the frequency of pathogenic races of Pyricularia oryzae in multilines after infection of panicles and spikelets, we created a predictive model for race frequency that incorporates incompatible race–isoline infection types and tested the reliability of the simulation. Cultivars Koshihikari and Koshihikari Niigata BL, each carrying one of the blast-resistance genes Pik-s, Pia, Pii, Pita-2, Piz, Pik, Piz-t, Pib and Pib·Pii, were cultivated in pots, and inoculated with race 001.0, which has a compatible infection type only with Pik-s. Model parameters for infection of each variety were generated by evaluating the severity of panicle blast, the proportion of sporulating spikelets, and the number of spores produced. Ten trials were conducted using different combinations of 2 or 3 rice lines from 5 lines of Koshihikari and Koshihikari Niigata BL (Pik-s, Pia, Pii, Pita-2 and Piz-t) and 2 or 3 isolates of 3 different races (001.0, 003.0 and 007.0). The values estimated by the simulation model were close to the race frequencies from many trials, indicating that this model can be used to predict the race frequencies in panicles of multilines.