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Hypothyroidism in infants is caused by the insufficient production of hormones by the thyroid gland. Due to stress in the chest cavity as a result of the enlarged liver, their cry signals are unique and can be distinguished from the healthy infant cries. This study investigates the effect of feature selection with Binary Particle Swarm Optimization on the performance of MultiLayer Perceptron classifier in discriminating between the healthy infants and infants with hypothyroidism from their cry signals. The feature extraction process was performed on the Mel Frequency Cepstral coefficients. Performance of the MLP classifier was examined by varying the number of coefficients. It was found that the BPSO enhances the classification accuracy while reducing the computation load of the MLP classifier. The highest classification accuracy of 99.65% was achieved for the MLP classifier, with 36 filter banks, 5 hidden nodes and 11 BPS optimised MFC coefficients.