Secondary chromosomal aberrations in follicle center cell derived lymphomas (FCDL) usually involve gains and losses of genetic material and may be an important prognostic value. In the present study, we aimed to determine the power of comparative genomic hybridization (CGH) as compared to standard chromosome analysis (CA) to detect such secondary aberrations. The same lymph node cell suspensions prepared from 30 patients with FCDL were analyzed in parallel by CGH and CA based on R banding. In all, 73 discrepancies were found. Sixty-two imbalances were detected only by CA and 11 only by CGH. In cases with completely resolved karyotypes (n= 17), the median number of discrepancies between CGH and CA was one. However, when the karyotype was partially resolved (n = 12), the median was four (P < 0.01). Discrepant results were further studied by fluorescence in situ hybridization using locus-specific probes. These data confirm, that not only for the detection of balanced aberrations, but also for the detection of unbalanced aberrations in FCDL, standard chromosome analysis is still the 'gold standard'. In contrast, CGH is useful to detect chromosomal imbalances when no metaphases are found or no fresh material is available.