In an effort to explain the seismic stability of ancient free-standing multi-drum columns that support heavy epistyles together with the even heavier frieze atop, the paper studies the complex 3D dynamic response of two free-standing multi-drum columns capped with a freely supported epistyle. More specifically, first the paper compares the 3D dynamic response of a standalone multi-drum column with the response of two same multi-drum columns under an epistyle, by using the FE code MARC. Then, to study how the height of the epistyle affects the dynamic response of the system, parametric analyses were performed with epistyles of different heights. In all cases, the multi-drum columns were subjected to sinusoidal base excitations having different acceleration amplitudes and different frequencies to ascertain the characteristics of the excitations in which the height of the epistyle plays an important role in the response of the system. The 3D models, which consist of multi-drum columns with three drums and a capital and a freely supported epistyle on the top, are part of the colonnade system of the Gymnasium of Ancient Messene in Greece. From the study useful results were obtained concerning the role of the height of epistyle together with the characteristics of excitation to the stability of the system.