Ischemic paediattric stroke (IPS) is a relatively rare disorder of mixed aetiology that is unexplained in approximately 30% of cases. Prothrombotic disorders are recognized as a risk factor for the development of IPS, but potential genetic variations in prothrombotic risk factors have been analysed in a limited number of studies in specific populations or in adults, while in children they have been scarcely analysed or they have not been analysed at all. As the association of prothrombotic polymorphisms with IPS can differ depending on the geographic and ethnic categorisation of the population studied, and an additional increased risk is known in the presence of more than one prothrombotic risk factor, the aim of this study is to examine the association of individual polymorphisms in the genes coding clotting factors, platelet membrane glycoproteins and intermediate risk factors, and the potential of their joint association with the occurrence of IPS in children in Croatia depending on the type of IPS, age of onset and localization of the lesion. Genotyping of 21 polymorphisms in 13 candidate genes was performed in a DNA samples obtained from leukocytes after collecting residual peripheral blood samples from 185 children aged up to 18 years with confirmed diagnosis of arterial IPS (AIS) or cerebral venous sinus thrombosis (CSVT) and 185 healthy children matched by age and gender to children with IPS. Obtained results confirmed a higher frequency of AIS in boys and other subtypes, but not in perinatal AIS and CSVT. Also, it has been proven that different subtypes of IPS are caracterised by different genetic factors. Based on the obtained results, an algorithm of tested genetic risk factors for IPS was proposed to distinguish the risk of subtypes of the disease, which established a database of children with IPS in Croatia. The results of the proposed research expanded the previous knowledge about the potential role of the examined genetic variations in the aetiology of IPS in Croatia, with translational potential to the adult population.