Congenital stromal corneal dystrophy (CSCD) is characterized by stromal opacities that morphologically are seen as interlamellar layers of amorphous substance with small filaments, the nature of which has hitherto been unknown. CSCD is associated with truncating mutations in the decorin gene (DCN). To understand the molecular basis for the corneal opacities we analyzed the expression of decorin in this disease, both at the morphologic and the molecular level.Corneal specimens were examined after contrast enhancement with cuprolinic blue and by immunoelectron microscopy. Decorin protein from corneal tissue and keratocyte culture was studied by immunoblot analysis before and after O- and N-deglycosylation. The relative level of DCN mRNA expression was examined using Q-RT-PCR, and cDNA was sequenced. Recombinant wild-type and truncated decorin transiently expressed in HEK293 cells were analyzed by gel filtration and immunoblotting.The areas of interlamellar filaments were stained by cuprolinic blue. Immunoelectron microscopy using decorin antibodies revealed intense labeling of these areas. Both wild-type and truncated decorin protein was expressed in corneal tissue and keratocytes of affected persons. When decorin expressed in HEK293 cells was examined by gel filtration, the truncated decorin eluted as high molecular weight aggregates.Accumulation of decorin was found in the interlamellar areas of amorphous substance. The truncated decorin is present in CSCD corneas, and there is evidence it may aggregate in vitro. Thus, decorin accumulation appears to contribute to the stromal opacities that are characteristic of CSCD.