Balanced chromosomal translocations do not normally have phenotypic manifestation, but lead to increased risk of infertility, miscarriage and live-birth of chromosomally unbalanced offspring in carriers. The risk assessment of such outcomes in carriers of rare chromosomal abnormalities is complicated since limited information is available on the frequencies of unbalanced sperm and embryo formation. Therefore, the aim of this study was to investigate the amount of normal/balanced and unbalanced sperm and embryos of a rare non-Robertsonian chromosome fusion carrier with karyotype 45,XY,der(5;15)(q35.3;q10). Cytogenetic analyses of peripheral blood lymphocytes, multicolour fluorescence in situ hybridization on sperm sample, trophectoderm biopsy, and preimplantation genetic diagnosis by array comparative genomic hybridization were performed. The most frequent type of meiotic segregation was alternate (53% in sperm and 66.7% in embryos), followed by adjacent (44% in sperm and 33.3% in day-5 embryos). Additionally, 3:0 segregation was detected in sperm with a frequency of 2.6% and not detected in day-5 embryos. Results of sperm segregation analysis in rare rearrangement carriers are valuable for genetic counselling in assisted reproduction.