Bicuspid aortic valve (BAV) is a common congenital heart diagnosis and is associated with aortopathy. Current guidelines for aortic resection have been validated but are based on aortic diameter, which is insufficient to predict acute aortic events. Clinical and translational collaboration is necessary to identify biomarkers that can individualize the timing of prophylactic surgery for BAV aortopathy. We describe our multidisciplinary BAV program, including research protocols aimed at biomarker discovery and results from our longitudinal clinical registry. From 2012–2018, 887 patients enrolled in our clinical BAV registry with the option to undergo four dimensional flow cardiovascular magnetic resonance imaging (4D flow CMR) and donate serum plasma or tissue samples. Of 887 patients, 388 (44%) had an elective BAV-related procedure after initial presentation, while 499 (56%) continued with medical management. Of medical patients, 44 (9%) had elective surgery after 2.3 ± 1.4 years. Surgery patients’ biobank donations include 198 (46%) aorta, 374 (86%) aortic valve, and 314 (73%) plasma samples. The 4D flow CMR was completed for 215 (50%) surgery patients and 243 (49%) medical patients. Patients with BAV aortopathy can be safely followed by a multidisciplinary team to detect indications for surgery. Paired tissue and hemodynamic analysis holds opportunity for biomarker development in BAV aortopathy.