The exposure to low LET-radiation leads to a relative homogeneous distribution of initial damage at the DNA. Subsequent repair and post-repair mechanisms might lead to a selection of specific breakpoint locations along chromosomes. Cells from patients with increased radiosensitivity may have more specific breakpoints due to impaired repair mechanisms. We tested whether cells from patients with increased radiosensitivity had an increase in specific breakpoint clusters. Structural chromosomal aberrations of in vitro irradiated lymphocytes from 11 healthy individuals and another 3 patients with increased radiosensitivity were examined. The chromosome pairs 1, 2, and 4 were treated using the three-color FISH technique. The breakpoints were analyzed by means of computerized imaging software. In total, 1752 chromosomal breakpoints had been considered, 498 from healthy individuals, and 1254 from patients with increased radiosensitivity. For both groups there was a non-homogeneous breakpoint distribution along the chromosomes and a trend towards increased breaks in the telomere-proximal region. Also, both groups had distinct locations with increased breaks. No evidence for significant breakpoint patterns across all patients with increased radiosensitivity was found.