Integration of heterogeneous information resources has been one of the most important issues in recent advanced application environments. In addition to conventional databases, structured documents have been recognized as important information resources recently. In this paper, we first present a data model named the NR/SD model as a basic data modeling framework for integration of structured documents and relational databases. Then, we discuss the query processing and optimization scheme for environments including structured document repositories and relational databases. The NR/SD model combines an abstract data type named the structured document type and the nested relational structures, and features operators named converters to dynamically convert structured documents into nested relational structures and vice versa. Therefore, we can manipulate information in either forms of structured documents and relations. This feature poses the following issues in query processing: (1) Utilization of the local query processing capability of the document repository and the relational database, and (2) Efficient manipulation of structured document data whose volume is potentially quite large. We discuss the query processing and optimization scheme mainly focusing on these issues.