The constitutively heterochromatic 1q12 band and the primarily euchromatic 17cen-p53 region comprise a similar size in terms of percentage of the total human genome but have a completely distinguishable chromatin structure. The aim of this study is to unravel whether this structural difference has an impact on the formation and processing of radiation-induced chromosome aberrations. To do so, we have analysed the initial induction and the long-term persistence of radiation-induced (3 Gy gamma-rays) chromosomal aberrations with breakpoints in either the 1q12 band or the 17cen-p53 region in comparison with the behaviour of the overall genome. The fusigenic potential of euchromatic and heterochromatic ends was also compared. This time course experiment was performed in a human lymphoblastoid cell line with sampling times at 1, 3, 7, 14 and 56 days after irradiation. The outcome of this study, with 68 000 metaphases studied by multicolour FISH, with centromeric (1cen and 17cen), paracentric (1q12) and locus specific (p53 gene) probes, revealed: (i) a similar radiosensitivity of all regions analysed irrespective of their chromatin configuration; (ii) a possible enhanced fusigenic potential of heterochromatic chromosome ends; (iii) a rapid decline of 1q12 translocations; and (iv) a similar long-term behaviour of translocations involving 1q12 and 17cen-p53. The implications of these findings in biomonitoring studies are discussed.