Two cases of nasopharyngeal cyst, in a two-year-old girl and a six-year-old boy, are described. The cysts were located in the right lateral wall of the nasopharynx in both cases. Histopathological examinations revealed that the cyst walls were lined with columnar epithelium. The positions of the cysts and pathological features indicated that they were of branchial origin, and they were assumed to originate in the second branchial pouch because of their anatomic location. They differed from previously reported cases in that they extended nearly to the base of the skull, occupying the parapharyngeal space. It was considered that they might have originated from the dorsal part of the second branchial pouch or the layer of endodermal cells cut off from the lower part of the eustachian tube.