Silicon (Si) fertilization improves crop cultivation and is commonly added in the form of soluble silicates. However, most natural plant-available Si originates from plant formed amorphous SiO2 particles, phytoliths, similar to SiO2-nanoparticles (SiNP). In this work we, therefore, compared the effect by sodium silicate and that of SiNP on Si accumulation, activity of antioxidative stress enzymes catalase, peroxidase, superoxide dismutase, lignification of xylem cell walls and activity of phenylalanine ammonia-Iyase (PAL) as well as expression of genes for the putative silicon transporter (PST), defensive (Tfgd 1) and phosphoenolpyruvate carboxykinase (PEPCK) and protein in fenugreek (Trigonella foenum-graecum L) grown in hydroponics. The results showed that Si was taken up from both silicate and SiNP treatments and increasing sodium silicate addition increased the translocation of Si to the shoot, while this was not shown with increasing SiNP addition. The silicon transporter PST was upregulated at a greater level when sodium silicate was added compared with SiNP addition. There were no differences in effects between sodium silicate and SiNP treatments on the other parameters measured. Both treatments increased the uptake and accumulation of Si, xylem cell wall lignification, cell wall thickness, PAL activity and protein concentration in seedlings, while there was no effect on antioxidative enzyme activity. Tfgd 1 expression was strongly downregulated in leaves at Si addition. The similarity in effects by silicate and SiNP would be due to that SiNP releases silicate, which may be taken up, shown by a decrease in SiNP particle size with time in the medium.