Dientamoeba fragilis is a common gastrointestinal parasite of humans; yet despite its discovery over 100 years ago, its mode of transmission is still a mystery. Recently a cyst stage of D. fragilis was identified in a rodent model of dientamoebiasis, which was also characterized using electron microscopy. While this clearly represents an incredible finding, one important question still remained: if these structures truly belong to D. fragilis, why have they not been identified in human specimens before? The presence of these structures in humans would greatly substantiate the existence of a cyst stage, given that humans are considered the preferred host of D. fragilis. To this end we carried out, a retrospective study in an attempt to identify the structures described by Munasinghe in human stool specimens. We identified both cyst forms, and putative precystic forms from human clinical samples. These forms were indistinguishable from the previously described. In light of the recent discovery of a D. fragilis cyst stage, and its substantiation by the observation of these structures in human stool specimens, attempts were made to identify putative cyst forming transcripts by mining the transcriptome of D. fragilis. A pathway for the formation of the D. fragilis cyst wall is proposed as well as some putative cyst wall proteins, based on their strong homology to proteins/genes implicated in the formation of the Giardia lamblia cyst wall.