Copy number variants are characterized by losses or gains of DNA sequences in a range from 50 base pairs (pb) up to several megabase (Mb) for each copy. The clinical significance of CNVs is classified according to the guidelines of the American College for Medical Genetics and Genomics. Benign copy number variants are widespread in the general population and have no clinical significance. As part of this research, a retrospective-prospective analysis was conducted based on results for 400 patients referred for diagnostic treatment for various types of neurodevelopmental disorders, in the period from September 2021 to May 2023. As part of the research, a register of benign CNVs of the Croatian population is established. The significantly higher frequency of benign CNVs on chromosome 14 (34.75% of the total number of variants) indicates a possible uniqueness within the Croatian population, while benign variants on chromosomes 13, 18 and 20 are almost absent. The distribution of duplications (72.55%) among 2288 variants is significantly more prevalent than deletions (27.45%). Benign variants encompassing segments or entire genes whose specific alleles are assocaited with different diseases (so called morbid genes) like FCGR3A, ATF6, TFG, NIPA1, TAP2, KANSL1 underscore the existence of non-clinically significant variations in coding and regulatory regions of the human genome. This registry represents an important resource not only for diagnostic purposes but also for future research on genomic variability in the Croatian population, providing a systematic insight into benign CNVs.