To validate a novel semi-automatic segmentation algorithm for MR-derived volume and function measurements by comparing it with the standard method of manual contour tracing. The new algorithms excludes papillary muscles and trabeculae from the blood pool, while the manual approach includes these objects in the blood pool. An epicardial contour served as input for both methods. Multiphase 2D steady-state free precession short axis images were acquired in 12 subjects with normal heart function and in a dynamic anthropomorphic heart phantom on a 1.5 T MR system. In the heart phantom, manually and semi-automatically measured cardiac parameters were compared to the true end-diastolic volume (EDV), end-systolic volume (ESV) and ejection fraction (EF). In the subjects, the semi-automatic method was compared to manual contouring in terms of difference in measured EDV, ESV, EF and myocardial volume (MV). For all measures, intra- and inter-observer agreement was determined. In the heart phantom, EDV and ESV were underestimated for both the semi-automatic. As the papillary muscles were excluded from the blood pool with the semi-automatic method, EDV and ESV were approximately 20 ml lower in the patients, whereas EF was approximately 16 % higher. Intra- and inter-observer agreement was overall improved with the semi-automatic method compared to the manual method. Correlation between manual and semi-automatic measurements was high (EDV: R = 0.99, ESV: R = 0.96; EF: R = 0.80, MV: R = 0.99). The semi-automatic method could exclude endoluminal muscular structures from the blood volume with significantly improved intra- and inter-observer variabilities in cardiac function measurements compared to the conventional, manual method, which includes endoluminal structures in the blood volume.