Based on farm field plot level survey data and laboratory test, we examine the determinants of the expression of Bt toxin in China's Bt cotton production. The results show that the expression of Bt toxin differs significantly among varieties. Even for the same variety the expression of Bt toxin also varies substantially among villages and among farmers in the same village. Econometric analyses show that after controlling for the effects of varieties and locations (or villages), farm management, particular applications of phosphate and potash fertilizers, and manure, has significant positive effects on Bt toxin expression in farmer's fields. In contrast to previous studies which showed that nitrogen fertilizer has a positive impact on expression of Bt toxin, this study shows that nitrogen fertilizer has no significant impact on expression of Bt toxin in farmer's fields. On the other hand, the expression of Bt toxin has a positive relationship with phosphate fertilizer, potash fertilizer and manure application.