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Carcinoma of unknown primary (CUP) is a malignancy without a clinically identified site of primary occurrence despite an appropriate diagnostic workup. CUP portends a poor prognosis with median overall survival ranging between 4–9 months. The utilization of cell-free DNA (cfDNA) for characterizing disease-site specific methylation signatures has, to date, been limited. We report a series with five participants with CUP from the Oregon Health and Science University (OHSU) who were enrolled in a study utilizing a multi-cancer early detection (MCED) test using cfDNA to detect the primary malignancy. The observations from our case series suggest that the utility of cfDNA should be further explored in patients with CUP, and a large prospective trial is needed.