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This paper proposes to use a convolution kernel over parse trees to model syntactic structure information for relation extraction. Our study reveals that the syntactic structure features embedded in a parse tree are very effective for relation extraction and these features can be well captured by the convolution tree kernel. Evaluation on the ACE 2003 corpus shows that the convolution kernel over parse trees can achieve comparable performance with the previous best-reported feature-based methods on the 24 ACE relation subtypes. It also shows that our method significantly outperforms the previous two dependency tree kernels on the 5 ACE relation major types.