Phosphorus (P) is a macronutrient playing important roles in many plant processes. Significant interest has been devoted to search and utilize genotypic variations in P use efficiency in rice but with little effort to understand its physiological and biochemical bases. In this study, we examined responses to P deprivation of some primary and secondary traits in 3-week-old seedlings of the three genotypes, Sobi-byeo (japonica), Dasan-byeo (japonica ~times indica) and Palawan (indica). In general, percent weight due to root was increased up to 26%, but amounts of root protein and proteins secreted from roots were decreased by 11 to 19% and 31 to 51 %, respectively, by 3 to 21 days of P deprivation in the three genotypes. Interestingly, however, responses of Palawan to short-term P deprivation were contrasting to those of Dasan-byeo and Sobi-byeo in seedling weight and contents of shoot protein, chlorophyll and anthocyanin. Seedling weight was not decreased, but shoot protein content was decreased in P-deprived seedlings of Palawan. Contents of chlorophyll in leaves and anthocynin in roots were increased in Dasan-byeo and Sobi-byeo, but decreased in Palawan. The results suggest that responses of protein and pigment synthesis to P deficiency are different in modem and traditional varieties and the difference may at least in part be due to the selection for high yield under highly fertilized conditions.