Degenerative valve disease is on the rise with greater than 100,000 valve operations performed in the US alone per year. The majority of those procedures employ tissue bioprostheses to avoid the attendant risk of anticoagulation, especially in the elderly. Though traditionally this approach has been considered a superior option to avoid anticoagulation, more recent analyses have demonstrated a significant incidence of previously unrecognized thrombosis associated with bioprosthetic valves, especially with the more recent advent of the transcatheter aortic valve replacement implantations. Bioprosthetic valve thrombosis is a major cause of either acute or indolent bioprosthetic valve degeneration, and often has an elusive presentation causing delayed recognition and treatment. The literature has extensively addressed the risks and benefits of anticoagulation following bioprosthetic valve replacement to prevent bioprosthetic valve thrombosis (BPVT), without conclusive evidence-based recommendations. The duration of anticoagulation following an episode of BPVT is unclear, and lifelong anticoagulation has been suggested. The increasing use of transcatheter aortic valve replacement as an alternative to surgical aortic valve replacement in various risk groups has introduced new challenges with regards to valve thrombosis, which have been poorly studied with regards to optimal treatment and prevention. The increasing use of valve-in-valve procedures is expected to bring on further uncharted challenges.