Background: Endoscopic Third Ventriculostomy (ETV) is considered an alternative to ventriculo-peritoneal (VP) shunt insertion to avoid the shunt complications. To improve the outcome of the infants with congenital hydrocephalus (HCP) through using adjuvant tools with endoscopic third ventriculostomy, which are transcranial Doppler and CSF flowmetry to assess the flow through the ventriculostomy. Objectives: Primary objective was to assess the clinical and radiological outcomes of endoscopic third ventriculostomy in cases of hydrocephalus below two years. Secondary objective was to assess the early and late complications associated with ETV during follow up study. Subjects and methods: This uncontrolled clinical trial included children with congenital HCP attended the Outpatient Neurosurgery Clinics, Suez Canal University Hospitals. Twenty patients, divided into 2 groups: Group I included congenital aqueductal stenosis patients and group II that included patients with Chiari II malformations, using Transcranial Duplex, CT brain and MRI CSF Flowmetry. Results: Patients of hydrocephalus with aqueductal stenosis, after ETV, had statistically higher stroke volume than those suffered from Chiari II pathology (p=0.008) and elicited a statistically reduction in peak systolic velocity (p=0.001), pulsatility index (p=0.001) and mean maximum velocity (p= 0.005). Patients with congenital hydrocephalus of Chiari II pathology had higher rate of complications than that of aqueductal stenosis (p=0.015). Success rate was higher among cases with aqueductal stenosis than in Chiari II pathology (p=0.007). Conclusion: ETV is a safe and effective technique for managing infants with congenital hydrocephalus due to aqueductal stenosis. MRI CSF flowmetry is a reliable method for evaluating the patency of a third ventriculostomy.