RFX (Redundancy Free XML) storage is a layered approach that provides compaction to XML. The non tree based RFX structure facilitates effective querying and maintenance of the XML databases with a substantial increase in compaction and reduced complexity. This paper presents security architecture for enforcing protection of the compact storage structure through client endorsement, consent module and selective encryption. Selective encryption is a novel technique developed for the same and plays a pivotal role in effective fortification of the RFX compact storage from intrusions. © 2008 IEEE.