Skew correction algorithm is indispensable in fully automated microarray image processing. Since most previous image skew correction algorithms for microarray were time-consuming,a fast skew correction algorithm was proposed based on Cellular Neural Networks(CNN). The first step was to obtain the center points of all spots by applying a series of CNN templates. The second step was to find out the skew angle by performing Hough transform and calculating deviation. The final step was to correct skew by CNN grey-scale image rotation template. Our algorithm utilized the parallel processing attributes of CNN and the characteristics of microarray image. Experiment results and theoretical analysis show that the algorithm works accurately and fast.