Collagen is the main structural element of connective tissues, and its favorable properties make it an ideal biomaterial for regenerative medicine. In dental medicine, collagen barrier membranes fabricated from naturally occurring tissues are used for guided bone regeneration. Since the morphological characteristics of collagen membranes play a crucial role in their mechanical properties and affect the cellular behavior at the defect site, in-depth knowledge of the structure is key. As a base for the development of novel collagen membranes, an extensive morphological analysis of four porcine membranes, including centrum tendineum, pericardium, plica venae cavae and small intestinal submucosa, was performed. Native membranes were analyzed in terms of their thickness. Second harmonic generation and two-photon excitation microscopy of the native membranes showed the 3D architecture of the collagen and elastic fibers, as well as a volumetric index of these two membrane components. The surface morphology, fiber arrangement, collagen fibril diameter and D-periodicity of decellularized membranes were investigated by scanning electron microscopy. All the membrane types showed significant differences in thickness. In general, undulating collagen fibers were arranged in stacked layers, which were parallel to the membrane surface. Multiphoton microscopy revealed a conspicuous superficial elastic fiber network, while the elastin content in deeper layers varied. The elastin/collagen volumetric index was very similar in the investigated membranes and indicated that the collagen content was clearly higher than the elastin content. The surface of both the pericardium and plica venae cavae and the cranial surface of the centrum tendineum revealed a smooth, tightly arranged and crumpled morphology. On the caudal face of the centrum tendineum, a compact collagen arrangement was interrupted by clusters of circular discontinuities. In contrast, both surfaces of the small intestinal submucosa were fibrous, fuzzy and irregular. All the membranes consisted of largely uniform fibrils displaying the characteristic D-banding. This study reveals similarities and relevant differences among the investigated porcine membranes, suggesting that each membrane represents a unique biomaterial suitable for specific applications.