Pueblo Bonito is divided into two sections by a precisely aligned wall, running north to south, through the central plaza. A Great Kiva is placed on either side of the wall, creating a symmetrical pattern common to many of the Great Houses. In addition to the great kivas, over thirty other kivas or ceremonial structures have been found, many also associated with the large central courtyard. Interior living spaces were quite large by the standards of the Ancient Pueblo.
The site covers almost two acres (8,000 m²) and incorporates at least 650 rooms, with some estimates rising to 800. In parts of the village, the tiered structure was four and five stories high. During later construction, some lower level rooms were filled with debris to better support the weight of the upper levels. The builder's use of core and veneer architecture and multi-story construction produced massive masonry walls as much as three feet (1 m) thick.