This work presents the diagnosis of iris nevus using a convolutional neural network (CNN) and deep belief network (DBN). Iris nevus is a pigmented growth (tumor) found in the front of the eye or around the pupil. It is seen that racial and environmental factors affect the iris color (e.g., blue, hazel, brown) of patients; hence, pigmented growths may be masked in the eye background or iris. In this work, some image processing techniques are applied to images to reinforce areas of interests in them, after which the considered classifiers are trained. We describe the automated diagnosis of iris nevus using neural network-based systems for the classification of eye images as ''nevus affected'' and ''unaffected''. Recognition rates of 93.35% and 93.67% were achieved for the CNN and DBN, respectively. Hence, the systems described in this work can be used satisfactorily for diagnosis or to reinforce the confidence in manual-visual diagnosis by medical experts.