Midline carcinomas associated with the nuclear protein in testis (NUT) gene rearrangement are rare, aggressive tumors that have been diagnosed most commonly in the head, neck, mediastinum, and upper aerodigestive tract. The ultrastructural features associated with this tumor have thus far received only brief comment and have never been illustrated. The authors provide a more extensive description and illustrate the electron microscopic findings in a typical case of NUT midline carcinoma, confirmed by cytogenetic and fluorescence in situ hybridization studies. This tumor was composed of cells displaying large, irregularly shaped nuclei with prominent compact nucleoli and abundant cytoplasm containing prominent bundles of tonofilaments, occasional clusters of pleomorphic granules, small numbers of lipid inclusions, and rare glycogen deposits. The cells exhibited stubby microvillous projections, were intermittently enveloped by basal lamina, and were interjoined by numerous well-formed desmosomal-type junctions and occasional junctional complexes. The authors propose that this constellation of ultrastructural features can prove helpful in discriminating NUT midline carcinoma from similar appearing entities.