Microsatellite instability (MSI) is a molecular landmark of mutations in DNA mismatch repair genes. The impaired efficiency of DNA repair mechanisms promotes carcinogenesis as well as contributes to tumour progression. Until now, only few studies on MSI in thyroid tumours have been published. Therefore, the aim of the present study was to investigate MSI as a possible characteristic feature of thyroid tumours. The analysis of 12 thyroid papillary carcinomas and 17 multinodular hyperplasias at 13 microsatellite loci showed MSI and loss of heterozygosity (LOH) in both types of lesion, with more alterations noted in the papillary thyroid carcinomas (in 65%) than in multinodular hyperplasia (in 35%). In carcinomas, LOH occurred more frequently than MSI, while in multinodular hyperplasia the LOH/MSI ratio is almost equal.