Intracranial germ cell tumors are rarely seen and typically localize in the pineal or suprasellar region. The largest category of germ cell tumors is the germinoma. There have been reported associations of malignant tumors and chromosomal abnormalities in germ cell tumors. In this study, we present a 22-year-old man with multiple congenital melanocytic nevi in association with pineal tumor. Congenital melanocytic lesions greater than 2 cm were counted to be 54 in number, and those smaller than 1 cm in diameter were found to be 25 in number. The pathological diagnosis of the pineal tumors was germinoma, and the lesions located in the occipital region and trunk were compound congenital nevi. To our knowledge, a relationship between multiple congenital melanocytic nevi and germ cell tumors has not been reported before. The connection between them remains to be clarified.