Purpose Complex chromosomal rearrangements (CCR) are rare rearrangements involving more than two chromosomes and more than two breakpoints. CCR are associated with male infertility as a result of the disruption of spermatogenesis due to complex meiotic configurations and the production of chromosomally abnormal sperm. We examined a carrier of a t(1:2:10) CCR in order to determine the patterns of segregation and any presence of an interchromosomal effect (ICE). Methods Centromeric, locus specific and telomeric probes (Vysis, USA) were used for the study. On~1,000 sperm nuclei from the reciprocal translocation carrier, dual color Fluorescence in situ hybridization (FISH) was performed on each of the involved chromosomes to determine the patterns of segregation. FISH was also performed on chromosome 13, 18, 21, X and Y to determine any ICE. Results We observed abnormal chromosome complements in 24.3%, 19.5% and 15.8% of sperm for chromosomes 2, 10 and 1, respectively. There was a significantly increased rate of ICEs for chromosomes 13 and 21 when compared with controls. Conclusions CCR may present a lower risk for producing unbalanced chromosomes than other studies have indicated.CCRs may be at an increased risk for ICE especially among acrocentric chromosomes.