In the human hippocampus, the pyramidal layer consists of the inferior aspect of the hippocampus which is organized segmentally. Each segment, together with granule layer of the dentate gyrus, exhibits structural unity. In humans, ellipsoidal protrusions called pyramidal hillocks (PHs), which consist of a thick pyramidal cell layer (PL), are present in the inferior aspect of the hippocampus, and are segmentally organized along a longitudinal axis. It is also known that the granule cell layer (GL) of the dentate gyrus (DG) is not a smooth but undulated structure. However, the cytoarchitectural relationships between the protrusions and undulation have yet to be studied well. Here, we aimed to clarify the three-dimensional cytoarchitecture of the PL and GL of human hippocampus. For that purpose, the GL and PL were three-dimensionally reconstructed from serial sections of human hippocampus stained with hematoxylin and eosin. The GL was shaped as tubing with an opening in the dorsal part, and undulated especially in the medial part, forming digit-like processes. In the base of a digit-like process, protrusions of the GL extended laterally, with longer ones reaching the lateral edge, whereas shorter ones disappeared around the medial 1/3 of the GL. Consequently, the lateral part of the GL was undulated loosely. In the ventral view of the PL, the ellipsoidal PHs were sagittally aligned, whereas in the top view, each PH formed an ellipsoidal trough. Each structural unit was formed by a trough of the PH along the bottom, and had a longer GL protrusion in the upper-center, and shorter GL protrusions located between the longer protrusions and the lateral edge of the GL. A digit-like process extended into a dens. It is concluded that a unit of the PH and the GL comprises the longitudinal segmental formation of the hippocampus.