Introduction Individuals with balanced translocations are estimated to be around 1 % of the patients with infertility. A reciprocal translocation usually involves breakage of two non-homologous chromosomes with exchange of fragment with different size. The medical history of affected couples includes abortions, stillbirth, congenital anomalies, possible mental retardation and unsuccessful IVF attempts. It is hard to define the exact risk of unbalanced karyotypes in gametes, but it is accepted that it could be more than 80%. Preimplantation genetic screening (PGS) is strongly recommended in cases with chromosome rearrangements allowing the study of female gamete segregation. Material and Methods In the present case we performed two IVF-PGS cycles in a couple with a 34 years old woman with karyotype 46 XX, t(1;16)(q12;q13). Altogether, 14 embryos on day 3 where biopsied and tested using the 24sure (Illumina Inc., USA) protocol for BAC arrays. Results Out of the 14 tested embryos only two were euploid, five embryos had unbalanced genome due to the involvement of the chromosomes with the parental translocation. The other embryos had ‘sporadic'aneuploidy. After the PGS an embryotransfer of two euploid embryos was performed with one healthy baby born. Discussion Commonly more than 60 % of embryos obtained from patients with reciprocal translocations carry abnormal chromosomal constitution and about 1:28/30 are normal. In this case the percentage of unbalanced embryos - 5/14 (∼ 36 %) was significantly lower than the expected according to the published data. However, other independent aneuploidies also co-exist, most of which are age dependent. Conclusions The theoretical percentage of embryos with unbalanced karyotypes and the data from the clinical practice after performing PGS in IVF patients with balanced translocations does not match in every case. The phenomenon reveals the need of additional studies about the molecular mechanisms of chromosomal segregation in human gametes and preimplantation embryos delivered from balanced translocation carriers.