In this paper, a new eigen-level data fusion model, whereby rough set data and a probabilistic neural network (PNN) are integrated using a data fusion technique, is proposed for structural damage detection. This model is used for structural damage detection and identification, particularly for cases where the measurement data has many uncertainties. More specifically, structural modal parameters derived from vibration responses are first discretized by the K-means clustering technique and the rough set technique is then employed to deal with the great volume of data and to extract optimal feature parameters. After that, the processed data and information are input to the fusion centre of the data fusion technique and fused with the PNN to give a fusion-based damage detection result. To verify the proposed method, two numerical examples are presented to identify both single and multi-damage case patterns. The effects of measurement noise and of non pre-processed rough set data on the damage detection results are also discussed. The results show that the proposed model not only has good damage detection capability and noise tolerance, but also significantly reduces data storage memory requirements and saves runtime as a consequence of the data fusion processing.