Base-isolation is regarded as one of the most effective methods for protecting the structural and nonstructural building elements from design level horizontal earthquake ground shaking. However, base-isolation as currently practiced does not offer unlimited protection for these buildings, especially when the ground shaking includes a strong vertical component. The vulnerability of nonstructural systems in a base-isolated building was made evident during recent shake table testing of a full-scale five-story base-isolated steel moment frame where nonstructural system damage was observed following tests including vertical excitation. Past research efforts have attempted to achieve 3D isolation of buildings and nuclear structures by concentrating both the horizontal and vertical flexibility at the base of the building that are either quite limited or not economically viable. An approach whereby the vertical flexibility is distributed up the height of the building superstructure to passively reduce vertical acceleration demands in base-isolated buildings is presented. The vertical flexibility is achieved by placing laterally restrained elastomeric ‘column’ bearings at one or more floor levels along the height of the building. To broadly investigate the efficacy of the vertically distributed flexibility concept and the trade-off between mitigation and cost, a multi-objective optimization study was conducted considering 3-story, 9-story, and 20-story archetype buildings that aimed to minimize the median peak vertical floor acceleration demands and to minimize the direct cost of column bearings. Based on the results of the optimization study, a practical rule for determining the number of levels and locations of column bearings is proposed and evaluated. Copyright © 2013 John Wiley & Sons, Ltd.