Protocols for pediatric germ cell tumors (GCT) allow for chemotherapy (CHT) initiation without histological diagnosis, based on typical clinical and radiological picture and increased alphafetoprotein (AFP) or beta-human chorionic gonadotropin serum levels. Such strategy may result in misdiagnoses in rare cases. We present two patients with abdominal tumors and high serum AFP levels, diagnosed as GCT. In both, no tumor shrinkage and increasing AFP was observed after first cycles of multidrug CHT for pediatric GCT. Histological examination of biopsied tumor tissues revealed metastatic cholangiocarcinoma in patient 1 and pancreatoblastoma in patient 2, which implicated immediate change of therapy. Presented cases support the necessity to consider the tumor biopsy when patients diagnosed with GCT based on typical clinical presentation and elevated AFP do not respond to CHT with AFP decrease and tumor size reduction.