Cytogenetic analyses of four squamous cell carcinomas (SCC) of the esophagus showed complex numerical and structural abnormalities. Chromosomal bands or regions preferentially involved were 11q13, 8q10, 21q10, 3p10 approximately p11, 1p11 approximately q11, 5p11 approximately q11, and 14p11 approximately q11. For the first time, to our knowledge, recurrent aberrations were identified in esophageal SCC, including homogeneous staining region (hsr), isochromosomes i(3q) and i(21q), and ring chromosome. Losses of chromosomal material dominated over gains. Recurrent imbalances included under-representation of 4p13 approximately pter, 5q14 approximately qter, 9p22 approximately pter, 10p, 11p13 approximately pter, 12p13 approximately pter, 17p10 approximately pter, 18p11 approximately pter, 21p, and 22p, as well as over-representation of 1q25 approximately qter, 3q, 7q, and 8q. Interestingly, hsr at different chromosomal regions occurred in three of four cases. With the application of fluorescence in situ hybridization (FISH) and multicolor combined binary ratio labeling-FISH with specific DNA probes, it could be shown that in two cases the hsr was derived from chromosome 11 material and that the amplicon included CCND1. Our results, together with previous molecular genetic findings, indicate that CCND1might be a prime target in 11q13 amplification, and that amplification of this gene might be crucial in the tumorigenesis of esophageal SCC. These observed chromosomal aberrations and imbalances thus provide important information for further molecular genetic investigation of esophageal SCC.