As interest in natural biogenic silica nanoparticles (NPs) from rice husks grows, it is important to know how their preparation (i.e., combustion, acid leaching, or alkali extraction) impacts their biocompatibility. Acid leaching and alkali extraction both generated highly pure silica NPs (>99.1% SiO2 vs 93.1% with combustion). However, toxicity tests with six different human and mouse cell lines found alkali-extracted silica NPs were the least harmful; for example, the concentration leading to 50% loss in viability (LC50) was typically around 500, 500-2000, and >2000 mg/L for the combustion, acid-leached, and alkali-extracted silica NPs, respectively. To mimic the presence of carbon during calcination (900 degrees C for 6 h), polyethylene glycol (PEG) was incorporated in the alkali-extracted silica NPs prior to this step. This significantly increased their toxicities; that is, the LC50 dropped to between 500 and 2000 mg/L and was exacerbated further when calcination was performed at a lower temperature and time (550 degrees C for 2 h): LC50 values dropped to between 62.5 to 1000 mg/L. These results show that the biocompatibility of rice husk-derived silica NPs is negatively affected by the presence of residual carbon during calcination, but also that it can be significantly improved via alkali extraction.