Congenital erythrocytoses represent a heterogeneous group of very rare disorders. Genetic changes affecting all parts of the regulatory pathway of erythropoiesis, including oxygen sensing (EGLN1, VHL, EPAS1, EPO), erythropoietin (Epo) sensitivity (EPOR, JAK2, SH2B3) or hemoglobin oxygen affinity (HBB, HBA, BPGM, PKLR) had been described in patients with congenital erythrocytosis. Erythrocytosis can be associated with other clinical problems caused by the same underlying genetic change. Therefore, the identification of these mutations in patients with presumed congenital erythrocytosis may be very important for an adequate clinical management. However, in most published cohorts the underlying genetic cause of presumed congenital erythrocytosis has been identified in less than one third of the patients. The use of NGS panel diagnostics and whole genome sequencing approaches may fasten the diagnostic process and contribute to fill the diagnostic gaps in these patient cohorts.