Abstract. Mitral valve regurgitation replacement could be benefited by the use of pre-surgical 3D models that would allow the clinician to better understand the patient's structural and functional information before surgery. As no single image modality can provide all this information, it is necessary to fuse 3D transthoracic echo (TTE) and magnetic resonance imaging (MRI) to obtain a complete model. The registration of these two modalities, within the context of cardiac imaging, is a challenging task that requires manual intervention or the use of anatomical landmarks that can drive the registration. Within the context of mitral valve planning, the papillary muscles represent an ideal landmark set as they can be clearly identified in both modalities. However, to date little work has addressed the problem of papillary muscle segmentation. In this paper, we apply an atlas-based segmentation method for the automatic extraction of papillary muscles from MRI. Results show that a good quality segmentation (Dice score 0.67 ± 0.13) can be achieved within the straightforward pipeline provided by this approach. Hence, our atlas-based segmentation method could represent the first key step towards a novel TTE-MRI fusion algorithm.