"Protein Folding Problem" is considered to be one of the "Great Challenges of Computer Science" and prediction of disordered protein is an important part of the protein folding problem. Machine learning models can predict the disordered structure of protein based on its characteristic of "learning from examples". Among many machine learning models, we investigate the possibility of multilayer perceptron (MLP) as the predictor of protein disorder. The investigation includes a single hidden layer MLP, multi hidden layer MLP and the hierarchical structure of MLP. Also, the target node cost function which deals with imbalanced data is used as training criteria of MLPs. Based on the investigation results, we insist that MLP should have deep architectures for performance improvement of protein disorder prediction.