Quantitative aspects were investigated and compared for anatomical characteristics among compression wood (CW), lateral wood (LW), and opposite wood (OW) in the stem wood of Ginkgo biloba. Characteristics of each part were observed in the 5th, 10th, and 15th to 20th growth rings via optical and scanning electron microscopy. The crystalline characteristics were measured using an X-ray diffractometer. The microfibril angles (MFAs) were measured using the iodine method applied to the tangential section, as well as from the slopes of the pit apertures. The CW and OW showed similar tracheid lengths in the 5th and 10th growth rings; however, the CW was the shortest in the 15th to 20th growth rings. The CW showed the highest ray height and lowest ray number in each growth ring. The MFAs of the CW were greater than those in the LW and OW from both measurement methods. The MFAs obtained from the iodine method were smaller than that of the MFAs obtained from the pit aperture measurements. The CW had the lowest relative crystallinity in each growth ring, whereas the crystal width of the CW was the smallest in the 5th and 15th to 20th growth rings.