Papillary thyroid carcinoma (PTC) is a known radiation-induced tumor. Rearrangements in human chromosome 10 and in particular intrachromosomal exchanges are often associated with PTC formation. In this study we measured intrachromosomal exchanges in human thyroid follicular cells exposed to sparsely or densely ionizing radiation. Assuming that inversions in chromosome 10 are a biomarker of PTC risk, we estimated the relative biological effectiveness (RBE) of heavy ions using a molecular marker in vitro. The analysis of chromosomal aberrations was performed with the mBAND technique, which allows detection of both inter- and intrachromosomal exchanges. Our results do not show any significant increase in the yield of intrachanges in samples exposed to heavy ions compared to X rays. Within the constraints imposed by the experimental model we used, we conclude that heavy ions would not necessarily be more effective than X rays in the induction of thyroid cancer.