CLL is a heterogenous disease from a clinical as well as from a genetic point of view. In order to characterize CLL patients in detail we performed chromosome banding analysis and interphase FISH on 133 cases and analyzed the IgVH status, CD38 and ZAP-70 mRNA expression in parallel. Of the 133 samples that were included in this study, 126 (95%) could be successfully analyzed by cytogenetic banding techniques. 102 (81%) of the 126 samples showed chromosomal aberrations. In comparison, all 133 cases could be successfully analyzed by FISH with a rate of 79% aberrations like deletions of chromosomes 13q (57%, in 38% as sole abnormality), 11q (17%), trisomy 12 (13%), 6q (7%) 17p (6%) and translocations involving 14q32 (4%). 9 cases with a normal karyotype in conventional cytogenetics revealed genetic aberrations by FISH. Additional aberrations not included in the FISH panel of probes, were detected in 47 samples (37%) by conventional cytogenetics. The assessment of additional risk factors in our cohort of CLL patients revealed an unmutated IgVH status in 55%, a positive ZAP-70 expression in 57% and a CD38 expression ≥ 30% in 29% of the samples. ZAP-70 mRNA expression resulted in concordance with the IgVH status in 75% of the cases with the concurrence of ZAP-70 positive/unmutated IgVH or ZAP-70 negative/ mutated IgVH. Genetic poor risk factors like del(11q) and del(17p )correlated well with an unmutated IgVH status with 89% and 75% concordant cases, respectively and also CD38 expression resulted in a significant correlation with the IgVH status (p = 0.028, Fischer’s exact test). When analyzing the group of 47 samples with cytogenetic aberrations beyond the FISH panel in more detail, it was remarkable that a large number of 22 cases (47%) was characterized by a complex aberrant karyotype (≥ 3 unbalanced aberrations). The status of somatic mutations of the IgVH gene was available for 39 cases in that group with 74% having an unmutated IgVH-status. This value was significantly increased (p = 0.013) compared to the 44% of unmutated samples calculated from the panel of samples that were concordant in FISH and chromosome analysis (IgVH status was available in 57 cases). No significant correlations were obtained for ZAP-70 and CD38 expression with the different cytogenetic groups. Remarkable was also the incidence of unbalanced translocations in 22 cases, not picked up by the FISH probes, which were strongly associated with an unmutated IgVH-status (83%). In conclusion, a comprehensive laboratory work-up is necessary in order to obtain more insights into the pathophysiology of CLL and for individualized treatment approaches. Interestingly, CLL cases with a more complex karyotype (≥ 3 unbalanced aberrations) or with unbalanced translocations correlated with an unmutated IgVH status and might therefore represent a high risk group of patients.