Computational models of the fluid dynamics in the human heart are a powerful tool to investigate disease mechanisms and their impact on the blood flow patterns. These models can for example be used to assess alterations occurring in hypertrophic cardiomyopathy, which is a genetic disease that increases the risk of sudden cardiac death. To overcome the challenges of a moving mesh approach, we modeled the movement of the endocardial surface based on an immersed boundary method. The verification on a simple moving 2D geometry proved plausible results. The application to the dis- eased, hypertrophic heart geometry confirmed that the computation of the mesh movement is made possible with this approach.