This problems has already been reported for xerces2. (bugnum 3503) I would appreciate it if this gets fixed in xerces 1.4.4 also. Until recently, we were using jaxp 1.0 (and sun parser) to parse exactely the same stuff without any problems. After upgradinf to jaxp 1.1 (and xerces) we get errors because the DOM tree is full of (unwanted) '#comment' nodes. Thanks.