This paper performs a 3-dimensional dynamic response and damage analysis of masonry and masonry infilled RC frame structures to blast induced ground excitations. A two-storey masonry structure and a two-storey masonry infilled RC frame as well as a six-storey RC frame filled with masonry wall are used as examples in the study. A previously developed 2-dimensional continuum material damage model including the orthotropic elastic properties, strength envelope and damage threshold of masonry, is extended to 3-dimensions and applied to masonry. Another 2-dimensional material damage model developed for reinforced concrete structures is also extended to 3-dimensions for modelling RC damage to high-frequency ground excitations. These material damage models are programmed into the commercial software Autodyn3D as its user subroutines to perform the analysis. Damage patterns of different structures under different ground excitations are simulated and discussed. The ductility ratios of the masonry structure and the inter-storey drift of the masonry infilled RC frames to blast excitations are also calculated. Numerical results indicate that under the same ground motion, the two-storey masonry structure suffers the most severe damage as compared to the two-storey masonry infilled RC frame. The six-storey RC frame filled with masonry wall experiences the least damage. It also shows that a structure under high frequency ground motions suffers brittle failure and its damage is governed by the force or stress rather than the inter-storey displacement or ductility. The present results further verify the conclusions drawn in the previous studies based on the 2-dimensional numerical model and scale model tests, namely, structural responses and damage to high-frequency blast ground motions are dominated by high vibration modes. Therefore displacement response-based criteria such as ductility ratios and inter-storey drifts as commonly used in earthquake engineering for assessing structural performances cannot be directly applied to structures under blast ground motions. The present numerical results are also compared with those obtained from the 2-dimensional analyses. Discussions on the adequacy of the code specified as well as the empirical allowable blast ground vibration limit to structures are also made.