Cassava storage roots result from swelling of adventitious roots by secondary growth. In the present study we aimed to gain insight into the molecular processes occurring during cassava storage root formation. We report a comparative gene expression study in adventitious and storage roots in order to identify genes possibly related to storage organ formation. Our results revealed five genes with higher expression levels in secondary xylem of storage roots than adventitious roots. Among them, the Mec1 gene coding for Pt2L4 glutamic acid-rich protein and a putative RING Zinc Finger and LEA protein genes were strongly induced in secondary xylem tissue.