This paper presents an efficient input variable selection method using both principal component analysis(PCA) and adaptive partition mutual information(AP-MI) estimation. PCA which is based on 2nd order statistics, is applied to prevent a overestimation by quickly removing the dependence between input variables. AP-MI estimation is also applied to estimate an accurate dependence information by equally partitioning the samples of input variable for calculating the probability density function. The proposed method has been applied to 2 problems for selecting the input variables, which are the 7 artificial signals of 500 samples and the 24 environmental pollution signals of 55 samples, respectively. The experimental results show that the proposed methods has a fast and accurate selection performance. The proposed method has also respectively better performance than AP-MI estimation without the PCA and regular partition MI estimation.