Objective To evaluate the benefit of using three-dimensional transesophageal echocardiography (3DTEE) over conventional two-dimensional transesophageal echocardiography (2DTEE) in evaluation of various morphological features of atrial septal defect (ASD) and patent foramen ovale (PFO) during transcatheter closure. Methods This is an observational cross sectional study including 115 patients (45 PFO and 70 ASD patients) who underwent 2D/3DTEE guided transcatheter closure from April 2019 to October 2021 in cardiology department, Tanta university hospital. Results 70 ASD patients were divided into two groups; the pediatric age group (18 patients, mean age 9.05 ± 3.51 years) and the adult group (52 patients, mean age 39.3 ± 10.15 years). ASD morphology was simple in 12.9% and complex in 87.1% of patients, where 3DTEE was superior in the evaluation of posterior, infero posterior rims, fenestrated flimsy rims, aneurysm shape, orientation, and quality of its tissue. Procedural success was defined as complete defect closure with no complications. The procedure was successful in 68 and failed in 2 patients. 45 PFO patients were divided into two groups; the pediatric age group (14 patients, mean age 13.5 ± 3.25 years) and the adult group (31 patients, mean age 35.2 ± 4.5 years). PFO morphology was simple in 22.2% and complex in 77.8% of patients, where 3DTEE was superior in the evaluation of the exact PFO opening from the left atrium, additional fenestrations, aneurysm shape, orientation, and quality of its tissue. The procedure was successful in all patients. Conclusion 3DTEE guided transcatheter ASD/PFO closure provides an additional value over conventional 2DTEE in assessment of complex ASD/PFO morphology.