Among verity of diagnostic approaches suitable for clinical analysis of thyroid lesions, the two oncogenes (R-EGFR and Rcerb-B2) are believed to be of discriminative power. In a retrospectively collected patient material we have defined different lesion types (normal tissue, benign and malignant tumours). Those were taken as class definitions in analysis performed to assign discriminating performance. Standard multivariate statistics has not performed satisfactory partly due to the data distribution and partly due to presence of the noise. Therefore we have developed a method for the classification purpose, which was based on principle of minimising generalised classification error. Results of the separation between carcinoma and normal tissue reached accuracy 70%, other classification attempts ended up in poor results. In general, misclassifications could be explained with the data quality (noise) and, when it came to benign lesions, with responsiveness of the oncogenes to tumour tissues.