Venous thrombosis (VTE) in children is increasingly diagnosed, as advanced medical care has increased treatment intensity of hospitalized pediatric patients. The aim of this review was to summarize the data available and to discuss the controversial issue of thrombophilia screening in the light of the pediatric data available. Follow-up data for VTE recurrence in children suggest a recurrence rate between 3% (neonates) and 21% in individuals with unprovoked VTE. Apart from underlying medical conditions, recently reported systematic reviews on pediatric VTE (70% provoked) have shown significant associations between thrombosis and presence of protein C-, protein S- and antithrombin deficiency, factor 5 (F5: rs6025), factor 2 (F2: rs1799963), even more pronounced when combined inherited thrombophilias [IT] were involved. The F2 mutation, protein C-, protein S-, and antithrombin deficiency did also play a significant role at VTE recurrence. Although we have learned more about the pathophysiology of VTE with the increased discovery of IT evidence is still lacking as to whether IT influence the clinical outcome in pediatric VTE. It still remains controversial as to whether children with VTE or offspring from thrombosis-prone families benefit from IT screening. Thus, IT testing in children should be individualized.