Silicon (Si) is a beneficial element for rice, a typical Si-accumulating plant. Si is able to improve nutrient imbalance in rice, but the underlying physiological and molecular mechanisms for this effect are poorly understood. In this study, we investigated the interaction between Si and zinc (Zn) in rice by using a mutant (lsi1) defective in Si uptake and its wild type (WT, cv. Oochikara) in terms of toxicity and accumulation. Si did not alleviate high Zn-induced inhibition of root elongation in both mutant and WT. However, Si supply decreased Zn concentration in both the roots and shoots of the WT although similar effect was not observed in the lsi1 mutant. The root-to-shoot translocation and distribution in different leaves of Zn was not altered by Si in both the WT and lsi1 mutant. In the WT, Si supply at 0.2 mM for 7 days was able to decrease Zn concentration in the roots and shoots. Furthermore, Si supply with 1 mM for three days was required to decrease Zn accumulation because one day exposure to 1 mM Si did not show the effect. Si supply also resulted in decreased Zn in the root cell sap and xylem sap in the WT, but this effect of Si was not observed in the mutant. These results indicate that Si and Zn interaction did not occur in the solution and that high Si accumulation in the shoots is required to decrease Zn uptake. To confirm this, we performed a short-term (30 min) uptake experiment with stable isotope ⁶⁷Zn. The results showed that ⁶⁷Zn uptake was significantly decreased by Si in WT, but not in the mutant. Furthermore, pre-treatment with Si also showed similar effect. When grown in paddy field, lsi1 showed higher Zn concentration in the straw, husk and brown rice than the WT. These results lead us to propose that some Zn transporter genes involved in Zn uptake are down-regulated by Si accumulated in the shoots. Further work on characterization of Zn transporter genes are being undertaken.