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Germ cell tumors are a heterogeneous group of tumors that can present primarily as gonadal tumors in either a localized or metastatic pattern. Rarely these tumors can initially present at extra-gonadal locations, including the gastrointestinal tract. We report two young male patients who presented with nonspecific gastrointestinal symptoms caused by a mass lesion involving the duodenum. Pathologically, both were confirmed to be germ cell tumors; an unfamiliar initial presentation of germ cell tumors. In both cases, evidence of pre-existing gonadal tumor in the form of a testicular mass and a burned-out tumor with microlithiasis, in the first and second cases, respectively was detected following the confirmed diagnosis of extra-gonadal germ cell tumor. Each patient’s clinical course and outcome emphasizes the importance of a high index of suspicion, timely diagnosis, and appropriate management.