Three-dimensional (3D) image reconstruction technologies can reveal previously hidden microstructures in human tissue. However, the lack of ideal, non-destructive cross-sectional imaging techniques is still a problem. Despite some drawbacks, histological sectioning remains one of the most powerful methods for accurate high-resolution representation of tissue structures. Computer technologies can produce 3D representations of interesting human tissue and organs that have been serial-sectioned, dyed or stained, imaged, and segmented for 3D visualization. 3D reconstruction also has great potential in the fields of tissue engineering and 3D printing. This article outlines the most common methods for 3D tissue section reconstruction. We describe the most important academic concepts in this field, and provide critical explanations and comparisons. We also note key steps in the reconstruction procedures, and highlight recent progress in the development of new reconstruction methods.