A multi-classifier diagnostic system was designed for distinguishing between benign and malignant thyroid nodules from routinely taken (FNA, H&E-stained) cytological images. To construct the multi-classifier system, several combination rules and different mixtures of ensemble classifier members, employing morphological and textural nuclear features, were comparatively evaluated. Experimental results illustrated that the classifier combination k-NN/PNN/Bayesian and the majority vote rule enhanced significantly classification accuracy (95.7%) as compared to best single classifier (PNN: 89.6%). The proposed system was designed with purpose to be utilized in daily clinical practice as a second opinion tool to support cytopathologists’ decisions, when a definite diagnosis is difficult to be obtained.