The thrombocytopenia is found in 1%-5% of newborns. Depending on mechanisms of pathogenesis of thrombocytopenia is divided on immune and non-immune one. The reaction of of interaction between antibodies and antigens of superficial structures of cells are in the basis of immune destruction of thrombocytes. During intrauterine period and period of newborness auto-, trans- and alloimmune alternatives of development of thrombocytopenia can be observed. The neonatal alloimmune thrombocytopenia is registered with rate of 1 case per 800-1000 newborns. The study was targeted to developing algorithm of diagnostic of immune thrombocytopenia, detecting main diagnostic criteria, exploring clinical significance of results of laboratory tests. The methods of study included typing of genes of HPA system using polymerase chain reaction with detection of results in real-time mode, detection of compatibility of HPA-genotypes of mother and child using flow cytometry technique. The following criteria of diagnostic of neonatal alloimmune thrombocytopenia: 1. detection of incompatible combination of HPA genes in mother and child (HPA-1bb/HPA-1ab; HPA-5aa/HPA-5ab; HPA-15ab/HPA- 15ab); 2. detection in blood serum of mother antibodies adsorbing more than on 3% of thrombocytes of child; 3. absence of antithrombocyte antibodies in mother and child (coefficient of auto-sensitization is less than 5%). The immune genesis of thrombocytopenia is established in 40% 0f children with low number of thrombocytes at birth. In 50% of cases the cause was determined as anti-thrombocyte alloantibodies with diagnosis neonatal alloimmune thrombocytopenia. Also in 50% of cases decreasing of number of thrombocytes in children occurred as result of impact of autoantibodies of mother with diagnosis “transimmune thrombocytopenia”. The considered laboratory methods have high specificity and permit to properly diagnose immune causes of thrombocytopenia in newborns.