A recently published study has alerted the cardiovascular community to the existence of a significant and previously unrecognized risk of subclinical valve thrombosis following implantation of surgical and catheter-based bioprosthetic valves. The purpose of this article is to review our current understanding of this new clinical entity and to identify unanswered questions and areas for future research. Subclinical bioprosthetic valve thrombosis (BPVT) is a more common phenomenon than previously appreciated. It appears that the incidence of BPVT is higher following transcatheter aortic valve replacement compared with surgical aortic valve replacement. Four-dimensional computed tomography (CT) is the most sensitive imaging modality for detection of leaflet immobility and subclinical BPVT. Certain echocardiographic findings, such as increasing transaortic gradients, increased cusp thickness and abnormal cusp mobility, predict the presence of BPVT on four-dimensional CT. There is a growing body of evidence linking subclinical BPVT with premature valvular hemodynamic deterioration and structural valve degeneration. Furthermore, subclinical leaflet thrombosis may constitute a nidus for unrecognized subacute cerebral or other thromboembolic events. Oral anticoagulation seems effective in both the prevention and treatment of BPVT. Subclinical valve thrombosis is an important and underappreciated cause of early bioprosthetic valve failure. Although several recent studies have improved our understanding of this newly recognized clinical entity, a number of questions remain unanswered. Further studies are warranted to elucidate the true incidence of subclinical BPVT, its clinical consequences, as well as the optimal antithrombotic regimen following bioprosthetic valve implantation. The subgroups of patients at highest risk of BPVT will need to be identified for risk stratification purposes. Several ongoing clinical trials will shed some light on these important issues.