Traditionally high-grade polycrystalline silicon production is obtained by the Chemical Vapor Deposition (CVD) process in the so-called Siemens reactor. The problem of rod temperature control in such a reactor is broached in this work. An indirect estimation method of the polysilicon rod diameter and the temperature estimation by means of the rod electrical resistance are both proposed. The main issue to overcome is related to the intrinsically unsteady-state conditions of the Siemens reactor (and all the batch reactors as well). From this perspective, the problem of temperature measurement can be solved using the appropriate pyrometer, although the temperature at the center of the rod has still to be estimate numerically. The aim of this paper is to develop a novel adaptive control system for the Siemens reactor based on neuro-fuzzy approach for both the parameter tuning and the control loop itself. A comparative discussion between the proposed method and other advanced control techniques is proposed.