Nasopalatine duct cyst is a developmental non-odontogenic cyst caused by the entrapment of remnants during embryologic fusion. Only a few cases have reported the intraluminal amorphous calcification in these cysts. This case showed a well-demarcated, unilocular lesion containing calcifications, which were later turned out to be cartilage graft at previous surgery. We report here this case to emphasize the need for thorough medical history taking.