A method and a system defragment indexes in a relational database. The relational database contains a set of tables, in which each table contains a set of indexes, in which, for each index, a fragmentation parameter is associated indicating the fragmentation level of the index. The method includes the following steps: getting a list of the set of tables; for each table of the list, getting the fragmentation parameter associated to each index of the table; and depending on the value of the fragmentation parameter, defragmenting the associated index.