Cilia are common organelles present on nearly every cell in the mammalian body. Found either in large groups on a single cell or as solitary structures, cilia are classified into three basic categories: motile, primary, or nodal. Primary cilia are solitary organelles projecting from the surface of cells. These cilia lack the central pair of microtubules needed to generate motile force and are thus described as having a 9-0 pattern. Dentigerous cyst is the second most common type of odontogenic cysts. It is the most common developmental cyst of the jaws and is always associated with an impacted tooth. The origin of the cyst is not yet known. Recent studies have shown that loss of Ptch and Shh signalling pathways are involved in the cystogenesis of dentigerous cyst. The Shh signalling pathway is active in the primary cilia. Based on the presentation of a dentigerous cyst in an autosomal dominant polycystic kidney patient and the demonstration of primary cilia like structures on the cyst wall by using a scanning electron microscope, a new hypothesis for the pathogenesis of dentigerous cyst is proposed recently (Anoop U.R. et al, 2011). To test this hypothesis and to check whether this hypothesis can be applied to other odontogenic cysts, a scanning electron microscopic study was conducted including 5 cases each of dentigerous cyst, odontogenic keratocysts and periapical cysts. The results showed the presence of primary cilia like structures in all cases of OKC and DC but not in any of PA cysts. The absence of PC like structures in PA cysts shows that the pathogenesis of inflammatory odontogenic cysts is entirely different from developmental cysts. Keywords: primary cilia, dentigerous cyst, odontogenic keratocyst, periapical cyst, scanning electron microscope