Hospital-Based Health Technology Assessment (HB-HTA) tools seem to be effective in strategic planning in hospitals. The benefit they show in the decision-making phase of medical devices management, in their acquisition, implementation, or the whole life cycle is obvious. Health technology assessment more and more includes an application of the Total Cost of Ownership (TCO) method, but its systematic incorporation into HTA is not complete yet. TCO has many advantages, when the main benefit follows from the fact that it helps identify costs that otherwise would remain hidden. TCO can be applied e.g. in the case of supplier selection, when TCO can be included to the input criteria of the multiple-criteria decision analysis. TCO finds further utilization in investment assessment on the basis of a prediction of future cost items. The last discussed area of TCO application is within evaluations of projects that were already implemented using retrospective data. The paper opens three basic perspectives of the TCO method as a part of HB-HTA, and it systemizes suitable application of this approach providing five case studies. These examples offer procedures specific for healthcare facilities and draw attention to particular “hidden costs” of health technologies.