Routine cytogenetic analysis of B-cell chronic lymphocytic leukemia/small lymphocytic lymphoma (B-CLL/SLL) frequently fails to identify an abnormal clone due to the low rate of spontaneous mitoses and poor response to mitogen stimulation. Recent studies utilizing interphase fluorescence in situ hybridization (FISH) suggest that prognostically significant chromosomal abnormalities occur more frequently in B-CLL/SLL than has been previously recognized. The purpose of this study was to compare the chromosomal abnormalities detected by karyotyping and FISH in cases of B-CLL/SLL, and to correlate these with clinical features and survival. Seventy-two cases were studied for chromosome 3, 12 or 18 aneuploidy, and for rearrangements involving 11q13, 11q23, 13q14, 14q32 and 17p13. The median age of the patients was 54 years (range, 30-87 years). Clinical staging of B-CLL patients showed that 70% of the patients were Rai stage 0, 1, or 2, and 30% stage 3 or 4. Karyotyping identified chromosomal abnormalities in 31% of the cases, whereas FISH studies were abnormal in 72% of cases including 64% of the cases with normal karyotypes. The most common abnormalities were deletion 13q14 (46%), trisomy 12 (21%), and 14q32 rearrangements (21%). At diagnosis, patients with trisomy 12 were more likely to have a high LDH (P = 0.04), but no other significant differences in the clinical or laboratory features, Rai stage, or survival were found among patients with normal cytogenetics vs. those with chromosomal abnormalities. Univariate analysis showed that B-symptoms (P = 0.044), anemia (P = 0.0006), absolute lymphocytosis > or = 30,000/mm3 (P = 0.029), and Rai stage 3 or 4 (P = 0.0038) at initial presentation were associated with an increased risk of death, but only Rai stage 3 or 4 (P = 0.0038) was significant in multivariate analysis. Interphase FISH studies improve the cytogenetic diagnosis when performed in conjunction with karyotyping in B-CLL/SLL, but the prognostic relevance of various abnormalities could not be confirmed in this study.