In this chapter, a method for the pattern recognition is used to provide a better diagnosis for patients with abnormal eye movements. The real data of signals of two eye movements (up and down) of patients are obtained using a mindset ms-100 system. A new method which uses one intelligent algorithm for online pattern recognition is proposed. The difference between the proposed method and the previous works is that in other works, both behaviors (up and down) are trained with one intelligent algorithm, while in this work, up behavior is trained with one intelligent algorithm and down behavior is trained with other intelligent algorithm. This is because the multi-output system can always be decomposed into a collection of single-output systems with the advantage of using different parameters for each one if necessary. The comparison results of the proposed method using the adaline network, multilayer network, or the Sugeno fuzzy inference system are presented for online pattern recognition of two eye movements.