Current serum biomarkers for diagnosis and monitoring of malignant germ cell tumors (GCTs) show limited sensitivity and specificity. We previously observed that microRNAs of the miR-371∼373 and miR-302 clusters are overexpressed in all malignant GCTs, regardless of patient age, histologic subtype, or anatomic site, but are not reported to be coordinately up-regulated in other tumor types or disease states. Herein we show that levels of all 8 main members of the miR-371∼373 and miR-302 clusters were elevated in the serum of a 4-year-old boy at the time of diagnosis of yolk sac tumor. Levels returned to normal during an uneventful clinical follow-up, with kinetics similar to those of the conventional marker α-fetoprotein. We describe in detail the multiplex polymerase chain reaction protocol used to quantify serum microRNA levels, which is highly robust and reproducible. Our study indicates that miR-371∼373 and miR-302 cluster microRNAs are promising candidate biomarkers for improving disease monitoring (and potentially diagnosis) in malignant GCTs.