This article addresses the Anti-synchronization problem of a class of uncertain chaotic systems with nonlinear inputs in a drive response structure. The high complexity of the unknown parameters of system can provide a new approach for enhancing message security in chaos based encryption systems. With uncertain, advanced three dimensional Chen-Lee, Lorenz-Stenflo and Liu-Chen systems have been considered to demonstrate the anti-synchronization problem. Simulation results are presented to illustrate the effectiveness of the considered chaotic systems.