The oxidative reactivity of THF derivatives formed during THF/nC60 synthesis was evaluated with indigo dye as a model compound. The results showed that the formation of previously undetected oxidizing agents during THF/nC60 synthesis accounted for the degradation of indigo dye by THF/nC60 (THF/nC60/unwashed), while THF/nC60 after vigorous washing (THF/nC60/washed) and nC60 prepared without the use of THF were not reactive. gamma-Butyrolactone (GBL) was detected by GC-MS in the THF/nC60/unwashed as one of THF derivatives, but showed no reactivity with indigo dye. An organic peroxide was detected in the THF/nC60/unwashed by HPLC, and was reactive with indigo dye. This compound was found to also account for the elevated antibacterial and bactericidal activities of THF/nC60/unwashed on E. coli. Analysis by LC/(+ESI)MS and 1H NMR showed that the detected THF peroxide was tetrahydro-2-(tetrahydrofuran-2-ylperoxy)furan. The formation of THF peroxide during the preparation of aqueous stable C60 aggregates provides another potential explanation for the reactivity and oxidative stress mechanisms of THF/nC60 system reported in the literature, although it does not exclude the potential reactivity and toxicity of nC60 itself.