Primary immunodeficiency diseases (PIDD) are inherited disorders resulting from defects in diverse elements of the human immune system. Currently, more than 330 PIDDs have been described, and the molecular (genetic) bases for more than 320 of them are known. PIDD can be divided into nine different groups, including antibody (humoral) deficiencies, innate/intrinsic deficiencies, phagocytic system deficiencies, complement component deficiencies, combined (T and B cells) immunodeficiencies, syndromic combined immunodeficiencies, immune dysregulation disorders, autoinflammatory diseases and phenocopies of PIDD. In the PIDD group, primary antibody deficiencies are the most common group, and approximately 50% of patients with PIDD fall into this group of deficiencies. Congenital primary immunodeficiencies typically appear early in life, although late onset is gradually more identified. Affected patients usually present clinically with recurrent/ severe infections, or clinical pictures resembling various autoimmune or other diseases. An early diagnosis of congenital immunodeficiencies is necessary for transfer to specialized medical centers, and prompt commencement of the optimal treatment, including transplantation and enhanced outcomes. In this review, a general approach is described for the investigation of the most common groups of PIDD, outlining the most appropriate laboratory investigations when the clinician comes across typical clinical pictures and/or infections suggesting immunodeficiency.