The aim of the study was to investigate whether changes in the pattern of gene copy number and cell cycle were present passing from the two- to the three-dimensional cell culture system. We used three human colon adenocarcinoma cell lines grown two- and three-dimensionally. We analyzed morphology, karyotype, chromosomal gain and losses, and cell cycle. In three-dimensional cell cultures the growth is delayed and arrested in G1 phase without specific rearrangements in the three-dimensional cultures compared to the two-dimensional cultures. These data suggest that the differences between the two- and three-dimensional cell culture systems do not involve chromosomal rearrangements.