Validation is an essential step in evaluating the applicability of simulated ground motions for utilization in engineering practice and also provides valuable insights towards improving the simulation methodologies by highlighting specific limitations of simulation methods. Simulated ground motions can be validated with a range of model complexity, from a single degree of freedom (SDOF) through to complex 2D/3D systems. A novel analysis framework has been developed to infer the probable causative sources related to the discrepancies between observed and simulated ground motions. This framework enables differences in the response of a complex system to be correlated to the differences in simplified intensity measures as well as remaining “unexplained” variability. This procedure therefore, provides valuable feedback for improving the simulation methodologies by linking the identified biases to causative model assumptions. As a case study, validation of simulated ground motions was investigated by comparing the dynamic responses of two steel special moment frames (SMRF) subjected to the observed and simulated ground motions of 498 small-magnitude earthquakes (3.5≤Mw≤5.0) across New Zealand. The seismic responses of the structures are principally quantified via the peak floor acceleration and maximum inter-storey drift ratio. Overall, the results indicate that the majority of the bias between the observed and simulated responses can be explained by the difference of the spectral acceleration at the main modes of vibration contributed to the selected response. This study will be extended to consider higher magnitude events and various structural models.