Neoplasms of the ovary present an increasing challenge to the physician. Neoplastic ovarian cysts can resemble endometriomas in ultrasound imaging and need to be carefully considered in the differential diagnosis. We report the case of a woman with a strong family history of hereditary breast and ovarian cancer, who presented with a pelvic mass. The young girl refused oncogenetic counseling and genetic testing, even though she had a 50% a priori probability of being a BRCA1 mutation carrier. Pelvic magnetic resonance imaging (MRI) and a comparative analysis of the serum concentration of HE-4 and CA125 biomarkers provided accuracy and sensitivity in the diagnosis of a benign ovarian pathology. Based on this experience, we propose that the sensitivity of a screening program based on a HE4 and CA125 assay and MRI in high risk patients with mutations in the BRCA1 and BRCA2 genes may be considered a useful pre-operative tool for the differential diagnosis of pelvic masses.