Although both lignin and silica accumulate on cell walls and confer rigidity, mechanical strength, and resistance to pathogen invasion in rice, it remains unclear whether silicon deficiency affects lignin accumulation. We demonstrate that low silicon rice mutated in a silicon influx transporter, Lsi1, or a silicon efflux transporter, Lsi2, contained larger amounts of lignin in the rice straws. Furthermore, wild-type rice cultivated on low silicon media also accumulated larger amounts of lignin in shoots. Significant accumulation of guaiacyl lignin upon silicon deficiency was determined by nitrobenzene oxidation analysis. These data indicate a negative correlation between silicon accumulation and lignin deposition.