Intraosseous schwannoma is rare, and most commonly occurs in the mandible. Benign classic schwannomas commonly carry normal karyotypes admixed with aberrant near-diploid karyotypes with a few simple clonal chromosome changes, mainly numerical. No consistent chromosomal aberrations have been observed so far. It is unclear whether the chromosomal abnormalities are affected by the anatomic site of the tumor; however, we know of no cytogenetic reports on schwannoma in the oral area. This novel report of cytogenetic analysis of intraosseous schwannoma represents the fifth report on a new balanced translocation in schwannoma in general. We identified clonal t(2;13) in an intraosseous schwannoma of the mandible. The significance of t(2;13) in diagnosis or prognosis is not yet clear, and should be further examined by karyotyping of more schwannoma cases.