Successful negative selection of autoreactive T cells requires expression of maximum amount of epitopes representing all possible protein isoforms in the thymus. Absence of some possible protein spliceforms in the thymus due to realization of some, but not all splicing combination, may limit the negative selection. Here we show that about 25% of studied mouse genes with well-described alternative splicing event encode some epitopes hidden from thymus. For five out of 10 randomly selected genes with predicted "hidden" epitopes, namely, Add2, Dst, Golga7, Lmna, Nasp, these findings were confirmed experimentally. Thus, for approximately 10-15% of alternatively expressed genes, their splicing patterns in Thymus may limit the set of epitopes available for negative selection.