High resolution images are used as a basis for finite-element modeling of the middle-ear structures to study their biomechanical function. Commonly used imaging techniques such as micro-computed tomography (CT) and optical microscopy require extensive sample preparation, processing or staining using contrast agents to achieve sufficient soft-tissue contrast. We compare imaging of middle-ear structures in unstained, non-decalcified human temporal bones using conventional absorption-contrast micro-CT and using synchrotron radiation phase-contrast imaging (SR-PCI). Four cadaveric temporal bones were imaged using SR-PCI and conventional micro-CT. Images were qualitatively compared in terms of visualization of structural details and soft-tissue contrast using intensity profiles and histograms. In order to quantitatively compare SR-PCI to micro-CT, three-dimensional (3D) models of the ossicles were constructed from both modalities using a semi-automatic segmentation method as these structures are clearly visible in both types of images. Volumes of the segmented ossicles were computed and compared between the two imaging modalities and to estimates from the literature. SR-PCI images provided superior visualization of soft-tissue microstructures over conventional micro-CT images. Intensity profiles emphasized the improved contrast and detectability of soft-tissue in SR-PCI in comparison to absorption-contrast micro-CT. In addition, the semi-automatic segmentations of SR-PCI images yielded accurate 3D reconstructions of the ossicles with mean volumes in accord with volume estimates from micro-CT images and literature. Sample segmentations of the ossicles and soft tissue structures were provided on an online data repository for benefit of the research community. The improved visualization, modeling accuracy and simple sample preparation make SR-PCI a promising tool for generating reliable FE models of the middle-ear structures, including both soft tissues and bone.