Participation of clinical genetic laboratories in External Quality Assessment schemes (EQAs) is a powerful method to ascertain if any improvement or additional training is required in the diagnostic service. Here, we provide evidence from recent EQAs that the competence in recognizing and interpreting cytogenetic aberrations is variable and could impact patient management. We identify several trends that could affect cytogenomic competence. Firstly, as a result of the age distribution among clinical laboratory geneticists (CLGs) registered at the European Board of Medical Genetics, about 25-30% of those with experience in cytogenetics will retire during the next decade. At the same time, there are about twice as many molecular geneticists to cytogeneticists among the younger CLGs. Secondly, when surveying training programs for CLG, we observed that not all programs guarantee that candidates gather sufficient experience in clinical cytogenomics. Thirdly, we acknowledge that whole genome sequencing (WGS) has a great attraction to biomedical scientists that wish to enter a training program for CLG. This, with a larger number of positions available, makes a choice for specialization in molecular genetics logical. However, current WGS technology cannot provide a diagnosis in all cases. Understanding the etiology of chromosomal rearrangements is essential for appropriate follow-up and for ascertaining recurrence risks. We define the minimal knowledge a CLG should have about cytogenomics in a world dominated by WGS, and discuss how laboratory directors and boards of professional organizations in clinical genetics can uphold cytogenomic competence by providing adequate CLG training programs and attracting sufficient numbers of trainees.