The identification of patients with aggressive cancer who require immediate therapy is a health challenge in low- and middle-income countries. Limited pathology resources, high healthcare costs and large caseloads call for the development of advanced stand-alone diagnostics. Here, we report and validate an automated, low-cost point-of-care device for the molecular diagnosis of aggressive lymphomas. The device uses contrast-enhanced microholography and a deep learning algorithm to directly analyse percutaneously obtained fine-needle aspirates. We show the feasibility and high accuracy of the device in cells, as well as the prospective validation of the results in 40 patients clinically referred for image-guided aspiration of nodal mass lesions suspicious of lymphoma.