It is still unclear whether the procedures of assisted reproduction increase the risk of congenital malformations. Thus, it remains to be clarified whether an increased risk, if any, of congenital malformations in these children is caused by the procedure of assisted reproduction itself or by the underlying maternal and paternal background. From the genetic point of view, infertility patients seeking assisted reproduction have to be classified as a high-risk group. The prevalence of numerical chromosomal abnormalities is around 10% in these patients, compared with 0.85% in the general population. The prevalence of structural chromosomal abnormalities is around 0.1% in the general population and is increased up to 1% in patients seeking assisted reproduction. In addition, patients with microdeletions of the Y-chromosome or mutations in the cystic fibrosis transmembrane-conductance regulator gene are likely to be encountered at the fertility clinic. Therefore, genetic screening and counselling should be routinely offered to infertility patients. They also need to understand that parental factors can be transferred to offspring that would most likely not have been conceived by natural means.