Remnants of the branchial apparatus can produce lesions in the head and neck region in later life, often amenable to fine‐needle aspiration (FNA) diagnosis. Yet such remnants or rudimentary lesions can remain clinically undetected and can later interfere with the cytologic interpretation of other deep lesions of the neck, as the present case demonstrates. In this case the lesion, which by a subsequent resection turned out to be a neurilemmoma, had been adequately sampled by the FNA, yet the cytologic diagnosis was sidetracked by the presence in the specimen of immature squamous epithelial tissue fragments and other elements (multinucleated histiocytes, calcifications), on the basis of which the diagnosis of an epithelial lesion, likely malignant, was made. The neck surgery and a preceding endoscopic examination of the mouth, pharynx, and larynx did not identify such a lesion, but a detailed microscopic examination of the fibroadipose tissue between the tumor and the peripharyngeal region revealed the presence of epithelial microfragments with morphology partly corresponding to that of the FNA cytology, highly indicative of a branchiogenic lesion in the peripharyngeal region. The basic embryology of the branchial apparatus resulting in such defects is presented, as well as tentative guidelines for recognizing material deriving from accidental sampling of such lesions during FNA investigations of deep‐seated masses of the neck. Diagn. Cytopathol. 2000;22:157–160. © 2000 Wiley‐Liss, Inc.