This paper presents a new methodology of the over-the-air (OTA) assessment for vertically arranged multiple-input multiple-output (MIMO) array antennas. Particular emphasis is placed on how well handset MIMO antennas with a vertically arranged structure are characterized using the limited number of scatterers implemented in a fading emulator. First we studied the mechanism of the arrangement of scatterers on the variation of channel responses using a proposed three-dimensional analytical model. It is shown that the condition of a 3D-OTA with the prescribed parameters allows the correlation to be reduced, which permits the channel capacity to increase in the same manner that sufficient scatterers are distributed over the entire solid angle. Then the appropriate scatterers arrangement for a 3D-OTA instrument considering the number of DUT antenna elements and multipath characteristics is investigated. The analytical results show that a suitable scatterers arrangement can be determined for various conditions of multipath environments and numbers of array elements, and that the arrangement can be employed for designing an actual 3D-OTA apparatus.