Thiamine pyrophosphatase (TPPase) cytochemistry is an established method for specific labeling of the trans-Golgi cisterns in tissue sections. Herein, we combined this enzyme cytochemical method with array tomography using scanning electron microscopy (SEM), a new imaging technique based on collection of backscattered electron (BSE) images of consecutive resin-embedded sections on glass slides, to detect the entire three-dimensional (3D) organization of the Golgi apparatus with sufficient spatial resolution. As the signal intensity of BSE depends on the atomic number of the materials, lead precipitates confined to the trans-Golgi cisterns after TPPase cytochemistry were clearly observed by BSE-mode SEM. The mild fixative used for TPPase cytochemistry also enabled accurate identification of target gonadotropes in the composite pituitary tissue by immunocytochemical staining. By 3D reconstruction of the entire trans-Golgi cisterns based on serial ultrathin section images of tissues after TPPase cytochemistry, we detected ultrastructural differences in the 3D configuration of the Golgi apparatus between cerebellar Purkinje cells and pituitary gonadotropes. The appropriate combination of enzyme cytochemistry and/or immunostaining with array tomography will further clarify the relationship between the organization and functional states of the Golgi apparatus.The Golgi apparatus plays an essential role in posttranslational modifications such as glycosylation and proteolytic processing of secretory and lysosomal proteins (14,22,26,48).This organelle also functions as a sorting center for transporting tubulovesicular carriers between the rough endoplasmic reticulum (rough ER) and the post-Golgi compartments destined for the lysosomes, secretory granules, and the cell membrane (1, 3, 5). The Golgi apparatus is generally composed of stacks containing several distinct layers of cisterns, designated as cis-, medial-, trans-cisterns in order from the entry side facing the rough ER (6, 7, 10). However, numerous studies also suggest that the overall three-dimensional (3D) organization of the intracellular Golgi apparatus varies with the cell type and their functional state (31,36,38,39,46). A wide variety of microscopic techniques have been developed to assess the organization and ultrastructure of the Golgi apparatus. Of these, scanning electron microscopy (SEM) is unique in providing invaluable information concerning the surface topography of specimens in biomedical fields. However, conventional SEM techniques alone are unable to visualize the detailed ultrastructure of intracellular organelles, including the Golgi apparatus, buried