A database system performs queries on fields storing arrays of a database (i.e., array fields) using de-duplication indexes. The system generates de-duplication indexes for array fields. The de-duplication indexes include unique entries for corresponding distinct values stored by the array fields. The system uses the de-duplication indexes to perform efficient queries specifying corresponding array fields. The system may further generate de-duplication indexes corresponding one or more fields storing various types of values. In various embodiments, the system selects an optimal index from various indexes usable to execute a query, such as a de-duplication index and a conventional index.