Several studies have demonstrated that nanoparticles (NPs) have toxic effects on cultured cell lines, yet there are no clear data describing the overall molecular changes induced by NPs currently in use for human applications. In this study, the in vitro cytotoxicity of three oxide NPs of around 100 nm size, namely, mesoporous silica (MCM-41), iron oxide (Fe 2 O 3 -NPs), and zinc oxide (ZnO-NPs), was evaluated in the human embryonic kidney cell line HEK293. Cell viability assays demonstrated that 100 µg/mL MCM-41, 100 µg/mL Fe 2 O 3 , and 12.5 µg/mL ZnO exhibited 20% reductions in HEK293 cell viability in 24 hrs. DNA microarray analysis was performed on cells treated with these oxide NPs and further validated by real time PCR to understand cytotoxic changes occurring at the molecular level. Microarray analysis of NP-treated cells identified a number of up-and down-regulated genes that were found to be associated with inflammation, stress, and the cell death and defense response. At both the cellular and molecular levels, the toxicity was observed in the following order: ZnO-NPs > Fe 2 O 3 -NPs > MCM-41. In conclusion, our study provides important information regarding the toxicity of these three commonly used oxide NPs, which should be useful in future biomedical applications of these nanoparticles.Key Words : MCM-41, Fe 2 O 3 nanoparticle, ZnO nanoparticle, HEK293, Microarray Introduction Nanoparticles (NPs) have increased surface area to weight ratios relative to the same materials in the non-nano size range. In addition to unusual physical properties, NPs are also more chemically reactive than larger particles, which can be either advantageous or harmful depending on their end use. The nanotech boom started around a decade ago and since then the use of NPs in consumer goods and biomedical applications has dramatically increased. NPs are increasingly applied as drug delivery vehicles, biosensors, imaging contrast reagents, and therapeutic agents. However, it is surprising that even today the scientific and industrial community has no sufficiently clear data on the overall effects of these NPs on human health.NPs are easily internalized into cells 1,2 and some NPs have even been shown to cross the blood brain barrier 3-5 where they alter biological processes and cause toxicity. Various in vitro and in vivo studies indicate that some NPs are associated with serious toxicity issues. The most commonly used in vitro toxicity tests focus on whether potentially toxic agents result in cell death. However, sublethal cellular changes may also exist that are not visible in such toxicity screens, but may significantly affect biological processes at the organismal level. Hence, it is important to identify overall cellular changes mediated by NP exposure. Identification of molecular signatures of toxicity at the genomic or proteomic levels provides comprehensive and reliable high throughput data. These data can then be used to compare, classify, and grade a NP on a scale of toxicity. In the present study we identified the m...