This is Volume II of a three volume set constituting the refereed proceedings of the Third International Symposium on Neural Networks, ISNN 2006. 616 revised papers are organized in topical sections on neurobiological analysis, theoretical analysis, neurodynamic optimization, learning algorithms, model design, kernel methods, data preprocessing, pattern classification, computer vision, image and signal processing, system modeling, robotic systems, transportation systems, communication networks, information security, fault detection, financial analysis, bioinformatics, biomedical and industrial applications, and more.