Thyroid gland
Congenital anomalies
Lymphoepithelial cyst

Author: Andrey Bychkov, M.D., Ph.D. (see Authors page)

Revised: 14 September 2015, last major update September 2015

Copyright: (c) 2015,, Inc.

PubMed Search: Lymphoepithelial cyst [title] thyroid

Cite this page: Lymphoepithelial cyst. website. Accessed January 19th, 2017.
Definition / General
  • Rare lesion which may arise from intrathyroidal remnants of branchial apparatus
  • Originally reported by Louis et al. in 1989 (Am J Surg Pathol 1989;13:45)
  • Branchial cleft remnants in thyroid become prominent in Hashimoto thyroiditis
  • Terminology
  • "Branchial cleft-like cyst": used for unusually located cervical lymphoepithelial cysts / branchial cleft cysts (i.e. not in soft tissue of anterolateral neck)
  • Also called branchial-like cleft cyst
  • Epidemiology
  • F: M = 2:1
  • Mainly adults (mean age 45 years, range 1 day to 73 years), 2 pediatric cases (see Case Reports)
  • < 40 cases published
  • Sites
  • Lateral thyroid
  • One case had unusual isthmic location (Thyroid 2010;20:111)
  • Pathophysiology / Etiology
  • Most authors link the origin of thyroid lymphoepithelial cysts to solid cell nests, which are the remnants of the ultimobranchial body
  • The most likely mechanism is squamous metaplasia and cystic degeneration of solid cell nests of the thyroid (Pathol Res Pract 1997;193:777)
  • The theory that intrathyroidal lymphoepithelial cysts arise from branchial remnants is supported by the occasional intrathyroidal presence of other branchial-derived structures, such as thymic and parathyroid tissue (Arch Pathol Lab Med 2003;127:e205)
  • An association with chronic lymphocytic thyroiditis is strong; immunological mechanisms responsible for the autoimmune thyroiditis may act on metaplastic epithelium or ultimobranchial rests to form the cysts and may explain the associated lymphoid infiltrate (Hum Pathol 1994;25:1238)
  • Alternatively, lymphoid tissue may be attracted by the presence of solid cell nests rather than by a primary autoimmune thyroidal process, because of their endodermal origin and inherited ability to form lymphoepithelial lesions (Pathol Int 2006;56:150)
  • Clinical Features
  • Either incidental finding of minimal clinical significance or presenting as a neck mass (Endo Pathol 1993;4:115, Hum Pathol 1994;25:1238)
  • Only a few cases (all pediatric) were not associated with concomitant thyroid disease, such as Hashimoto thyroiditis/chronic lymphocytic thyroiditis or nodular goiter
  • May coexist with thyroid cancer, but not related pathogenetically (Thyroid 2010;20:111)
  • Rarely causes hoarseness due to vocal cord palsy (Ann Acad Med Singapore 2010;39:68)
  • Diagnosis
  • Diagnosis occurs only after surgery (AJNR Am J Neuroradiol 2000;21:1340)
  • Workup includes radiological and pathological examination
  • Radiology Images
  • TBS / total body scan: cold nodule(s), rarely a hot nodule (Am J Surg Pathol 1990;14:1165)
  • US: hypoechoic or echogenic with pseudosolid appearance (AJNR Am J Neuroradiol 2000;21:1340), rarely solid (J Clin Ultrasound 2006;34:298)
  • MRI: multiloculated cystic nodule
  • Case Reports
  • Infant with intrathyroidal branchial cleft (Korean Journal of Pediatrics Vol. ;49:1005)
  • 7 year old girl with intrathyroidal branchial cleft-like cyst with heterotopic salivary gland-type tissue (Pediatr Dev Pathol 2004;7:262)
  • 36 year old woman with multiple branchial cleft-like cysts with Hashimoto thyroiditis (Endocr J 2000;47:303)
  • 42 year old man with multilocular lymphoepithelial cyst in the thyroid accompanied by a minute thyroid carcinoma (Pathol Int 1995;45:965)
  • 47 year old man with bilateral intrathyroidal lymphoepithelial cysts (Arch Pathol Lab Med 2003;127:251)
  • 50 year old woman with eosinophilic replacement infiltrates in cystic Hashimoto thyroiditis (Endocr Pathol 2014;25:332)
  • 50 year old man with branchial cleftlike cysts (Am J Otolaryngol 2006;27:146)
  • 55 year old woman with lymphoepithelial cysts of the thyroid gland (Arch Pathol Lab Med 2003;127:e205)
  • 54 year old woman with cytological features of a lymphoepithelial cyst (Soonchunhyang Med Sci 2014;20:131)
  • 65 year old man with branchial-like cysts of the thyroid associated with solid cell nests (Pathol Int 2006;56:150)
  • Intrathyroidal lymphoepithelial cyst (Pathol Res Pract 1997;193:777)
  • Amyloid goiter associated with intrathyroid parathyroid and lymphoepithelial cyst (Endocr Pathol 2009;20:243)
  • Bilateral lymphoepithelial cysts of the thyroid gland (Thyroid 2010;20:111)
  • Treatment
  • Surgical excision of the cyst; radical thyroid removal is not recommended (Thyroid 2010;20:111)
  • Clinical Images
    Missing Image

    Transverse sonogram of thyroid

    Missing Image

    Neck MRI, coronal view

    Missing Image

    Sonogram and CT

    Gross Description
  • Lateral lobe(s) of the thyroid
  • Solitary / multiple unilocular or multilocular cysts, usually 1 - 2 cm (few mm to 5 cm)
  • Smooth external surface, 0.1 - 0.2 cm thick wall; light-tan glistening lining with cobblestone appearance; clear or yellow viscous fluid (Am J Surg Pathol 1989;13:45)
  • Gross Images
    Missing Image

    Multilocular cyst

    Micro Description
  • The cyst structure is identical to branchial cleft cyst (Branchial pouch / cleft anomalies) composed of lymphoid tissue with germinal centers and squamous lining
  • Epithelial lining is attenuated stratified squamous (one or two cells to approximately seven cells in thickness) or focal respiratory-type epithelium with ciliated or goblet cells
    • Focally can be denuded
    • Cyst lumen contains keratin/mucin and debris with cholesterol clefts
  • Abundant adjacent lymphoid tissue, lymphoid follicles with prominent germinal centers common in cyst wall (Hum Pathol 1994;25:1238)
    • Old cysts have a rim of fibrous tissue
  • No thyroid parenchyma within the cyst, may have entrapped follicles in the outer side of cystic wall
  • Signs of thyroiditis (often florid Hashimoto thyroiditis) in surrounding thyroid (Am J Surg Pathol 1989;13:45)
  • Solid cell nests, basaloid squamous nests, and C-cell hyperplasia often found in surrounding parenchyma (Am J Surg Pathol 1989;13:1072, Am J Surg Pathol 1990;14:1165)
  • Micro Images
    Missing Image

    Squamous epithelium

    Missing Image

    Lymphoid follicles with germinal centers

    Missing Image

    Squamous epithelium lining

    Missing Image

    Dense lymphoid infiltrate

    Missing Image

    H&E, p63, Ki67

    Virtual Slides
    Missing Image

    Nodular left lobe of thyroid

    Cytology Description
  • Mature superficial squamous cells with intact nuclei, anucleate squames, clusters of neutrophils and lymphocytes, macrophages, amorphous debris in the background (AJNR Am J Neuroradiol 2000;21:1340)
  • Some cases yield solely lymphocytes (Endocr J 2000;47:303), squamous cells (Am J Otolaryngol 2006;27:146) or respiratory epithelium (J Clin Ultrasound 2006;34:298)
  • Cytology Images
    Missing Image


    Differential Diagnosis
  • Intrathyroidal thyroglossal duct cyst: midline location, thyroid remnants in cyst wall, no germinal centers (Am J Surg Pathol 1989;13:45)
  • Cystic tumors:
  • Cystic goiter
  • Cystic thymic remnants: basaloid cells with Hassall corpuscles (Arch Pathol Lab Med 2003;127:251)
  • The distinction from branchial cleft cyst rests on the finding of respiratory-type epithelium (Arch Pathol Lab Med 2003;127:251)
  • Cytology: