Background: This study investigated the relationship between training programmes for pandemic flu and level of knowledge of health-care professionals with performance in an avian flu exercise. Methods: Training programmes of all general hospitals in Israel for managing a pandemic influenza were evaluated. Spearman's ρ correlation was used to analyse the relationship between training scores and level of knowledge of medical personnel with performance in an avian flu exercise. Hospital preparedness levels were evaluated at two time points and Wilcoxon signed-rank test was used to determine if overall preparedness scores improved over time. Results: Evaluation of training programmes for pandemic influenza showed high to very high scores in most hospitals (mean 85, SD 22). Significant correlations between training and performance in the exercise were noted for: implementation of training programmes 0.91, P=0.000; designating personnel for training 0.87, P=0.000; content of training 0.61, P=0.001; and training materials 0.36, P=0.05. Overall reliability of the evaluation scores was 0.82 and reliability for two of the sub-scales was: implementation of the programme 0.78; and designating personnel for training 0.37. No significant correlation was found between level of knowledge and performance in the exercise. Discussion: Training programmes for hospital personnel for pandemic flu have a significant role in improving performance in case of pandemic flu. The key component of the training programme appears to be the implementation of the programme. Use of knowledge tests should be further investigated, as they do not appear to correlate with the level of emergency preparedness for pandemic influenza.