Epithelial tumors of the thymus are rare neoplasms typically arising in the anterior mediastinum. There is an ongoing discussion whether thymomas of different histological subtypes form a biological continuum or represent distinct biological entities. To further investigate this question, we performed a statistical analysis of CGH data of 65 previously published cases. Losses of 3p, 6p, 6q, 13q, 16q, and 17p, as well as gains on 1q, were found in at least 10% of the cases. Comparing the data from B2, B3, and C thymomas, we noted an increasing complexity of karyotypes that may be well explained by a sequential order of these types. The frequencies of losses on 16q and 17p show a significant trend with respect to the sequence from B2 to B3 and C thymomas, indicating that these aberrations may be important events in the transition between these tumor types. To identify pathways of genetic development and progression of thymomas, we used oncogenetic tree models representing the dependencies between recurrent chromosomal aberrations. This analysis suggests that gains on the long arm of chromosome 1 occur early in tumor development and are correlated with losses on 6p and 6q. There is a weak correlation with losses on 16q and 17p, which appear to be late events. An independent pathway leads to losses on 3p and 13q, which are closely correlated. Our results indicate that the development of thymomas seems to be in some part a multistep mechanism. Oncogenetic tree models are a helpful means to determine developmental pathways of tumors arising from the same progenitor cell, as shown here for thymomas.