Malignant germ cell tumors (GCTs) such as seminoma and yolk sac tumor cause serious health problems but with favorable prognosis if they were diagnosed timely. To investigate potential biomarkers used for GCTs diagnosis and phenotype distinguishment, we first applied a lncRNA classification pipeline to identify 368 lncRNAs represented on the Affymetrix Human Genome U133A Array. We then comprehensively analyzed the lncRNA expression patterns in a set of previously published gene expression profiles of seminoma and yolk sac tumor stratified by different age groups (children and adults). The lncRNAs expression signatures between children and adults in different GCTs phenotypic groups were identified respectively, five aberrantly expressed lncRNAs were shared by children and adults, indicating a role for them in distinguishing seminoma from yolk sac tumor regardless of age. In parallel, nine distinctive lncRNAs were also determined between seminoma and yolk sac tumor, which suggested that people may face a high risk of suffering from GCTs. Our findings may contribute to the early diagnosis and prognosis of GCTs regardless of patients' age and other diseases.