We present cytogenetic findings in five gastrointestinal stromal tumors (GISTs). Three of these five cases had abnormal karyotypes with clonal chromosomal aberrations. The most common karyotypic pattern was a combined loss of chromosomes 14 and 22 in a total of three cases. Among these cases, additional recurrent chromosomal abnormalities were loss of 1p and/or 9, detected in two cases each. Another karyotypic feature consisted of polyploidisation, leading to hypotetraploid chromosome numbers in one case. These cytogenetic results provide evidence for a characteristic karyotypic pattern consisting of -14 and -22 in a subset of GISTs.