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Embryology, Ear Congenital Malformations

Editor: Anoosh Zafar Gondal Updated: 5/1/2023 6:05:43 PM


The ear divides into three areas: the external, middle, and inner. Based on location, different malformations can present. A malformation is not only a change in appearance but also an alteration in function. External ear defects are common and occur in roughly 5% of the total population.[1] The most common malformations consist of combined external and middle ear deficits, called congenital aural atresia.[2] Microtia is a term used to describe the underdevelopment of the pinna, whereas anotia is a term used for an absence of pinna.


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External ear:

The pinna and external auditory canal are the main structures of the external ear. The pinna derives from the ectoderm, specifically from branchial arches 1 and 2. The external auditory canal forms from the 1st branchial groove.[2]

Middle ear:

The tympanic cavity and ossicles make up the middle ear. The tympanic cavity derives from the endoderm of the 1st pharyngeal pouch. The ossicles consist of three structures: the malleus, incus, and stapes. The malleus and incus come from the mesenchyme of the 1st branchial arch whereas stapes from the second branchial arch.[2]

Inner ear:

The inner ear develops from a thickened portion of the ectoderm close to the hindbrain.[3] The labyrinth has osseous and membranous parts. The osseous parts are from the ossification of the capsule, while the membranous part is from the neuroectoderm of the otic placode.[2]


Microtia is a common term used to describe a malformation in the pinna. The chondrocytes make up the outer ear, and research has determined that there are some differences in normal chondrocytes and those harvested from patients with microtia. These differences lead to decreased migration and resulting hypoplasia.[4]


External ear:

The gene expression markers involved in external ear growth include sox2, nestin, BST-1, and OCT4. Individuals with microtia demonstrate a reduction in these gene markers.[4]

Middle ear:

FGFR2 is a regulator of middle ear growth and controls the proliferation of cells. If there is a mutation in this growth factor, malformations may occur.[5]

Inner ear: 

Septin7 regulates the formation of the sensory epithelial area in the inner ear, but not the differentiation of the hair and supporting cells.[3] FGF3 and FGF10 are also needed, simultaneously, to produce the otic capsule, if one factor is missing, the other factor will compensate.[6]

Molecular Level

Stereocilia play an integral role in the inner ear. The core of a stereocilium consists of actin bundles. Stereocilia are linked together by linker molecules. Unconventional myosin is a subgroup of myosin that organizes and moves stereocilia with the use of transduction canals. Defects in unconventional myosin can lead to hearing loss.[7]


External ear:

The external ear's primary function is resonance and sound amplification.[8]

Middle ear:

The middle ear is a fluid-filled cavity in the skull that has three ossicles. The sequential order of ossicles transmits sound and vibrations from the tympanic membrane to the inner ear.[9]

Inner ear:

The inner ear includes the cochlea, the vestibule, and the three semicircular canals. The cochlea is responsible for hearing, while the vestibule and semicircular canals play a part in balance.[10]


External ear:

The outer pinna funnels the sound into the external auditory canal.[10] Because the external auditory canal is essentially a tube, it transmits the sound to the middle ear. If there is a malformation in the pinna, then there can be anatomical interferences leading do a decrease in resonance.[8]

Middle ear:

The tympanic membrane vibrates as a response to sound from the external auditory canal. These vibrations then transfer to the three ossicles, which then induce fluid vibrations of the cochlea of the inner ear.[9]

Inner ear:

Perilymph fluid is what fills the bony labyrinth, while endolymph is present in the cochlear duct and the membranous labyrinth. Endolymph vibrations stimulate the auditory receptors within the cochlea and vestibule. The endolymph affects the function of the vestibule and the auditory aspects.[10] When the endolymph of the cochlea receives the vibrations from the middle ear, these become electrical signals created by the organ of Corti (specifically the hair cells).[9] 

In regards to the auditory component of the inner ear, outer hair cells are three-quarters of the total number of sensory cells in the cochlea. Inner hair cells are associated with the displacement of the basilar membrane. These hair cells receive innervation from CN VIII. The inner hair cells are sensory only, while the outer hair cells are for mechanical feedback.

For the function of balance, the semicircular canals take precedent. The semicircular canals consist of the cristae within the ampullae and the maculae of the utricle and saccule. The utricle and saccule are the otolithic organs that are known for linear accelerations. The maculae and cristae have hair cells like the cochlea. In the maculae, the hair cells have otoconia in a gelatinous layer, so when the head moves, the otoliths change position leading to the excitement of hair cells. The semicircular ducts (besides the otolithic organs) are sensitive to head rotations. There is one horizontal and two vertical canals. While the head rotates, the endolymph moves in the ducts exciting the hair cells.[10]


External and middle ear region diagnostic imaging is usually via CT scans. Inner ear scanning is generally with an MRI or CT scan.[2]


There are different types of inner ear anomalies, and they currently get placed into categories numbered 1 through 7. These categories primarily have their basis on defects in the modiolus and the scala vestibule. Because there are several anomalies, there are many associated hypothesized pathophysiologies. Some, in particular, include high cerebrospinal fluid pressure, defective endosteum, large quantities of endolymph, and decreased cochlear vascular supply.[11]

Clinical Significance

External ear:

A few studies exist on epidemiological factors of anotia and microtia. A recent study in Japan found that approximately 60% of cases are male, and 85% are unilateral. Unilateral microtia presents in 1 per 10000 patients.[12] 

There are many syndromes associated with these outer ear malformations. Arguably, the external ear malformations lead to the most overall distress because of the cosmetic appearance. The most well known is Treacher Collins syndrome (TCS). This syndrome consists of disproportionate ears bilaterally that may present as rotated, and occur in 77% of patients with TCS. Along with external ear malformation, there is mandibular hypoplasia. These malformations occur together because both develop embryonically from the first and second branchial arches. Recent studies have shown that the ear malformations consist of roughly 50% decrease in ear volume, approximately 19% decrease in ear length, and about 28% decrease in ear width. Naturally, these external anomalies lead to a weakened self-confidence in these patients and result in problems with communication.[1]

Middle ear:

Cholesteatomas are the primary defect of the middle ear. Although these can be acquired, there are congenital cholesteatomas as well. Current theories include that they are the remaining remnants of embryonic epithelial tissue. These malformations are more common in males. The age of diagnosis is lower in congenital than in acquired cholesteatomas. Many patients do not have chief auditory complaints but receive a referral from the pediatrician due to the presence of a white mass behind the tympanic membrane.[13] Cholesteatomas are keratin-filled growths that can expand in 4 to 6 years. Surgery is the most common treatment. The condition is considered congenital when there are no symptoms, prior surgery, or previous injury. Other theories include retained epithelial rest cells. They can occur in various portions of the middle ear, so there can be many origin sites. They lead to tympanic membrane rupture, ossicle erosion, extension, and invasion.[14]

Inner ear:

About 20% of congenital sensorineural hearing loss is due to inner ear malformations. Cochlear implants are the treatment of choice but have been found to have variable clinical results.[11]



Ma X, Xie F, Zhang C, Xu J, Lu J, Teng L. Correlation Between Mandible and External Ear in Patients with Treacher-Collins Syndrome. The Journal of craniofacial surgery. 2019 Jun:30(4):975-979. doi: 10.1097/SCS.0000000000005216. Epub     [PubMed PMID: 31166254]


Kösling S, Omenzetter M, Bartel-Friedrich S. Congenital malformations of the external and middle ear. European journal of radiology. 2009 Feb:69(2):269-79     [PubMed PMID: 18054456]


Torii H, Yoshida A, Katsuno T, Nakagawa T, Ito J, Omori K, Kinoshita M, Yamamoto N. Septin7 regulates inner ear formation at an early developmental stage. Developmental biology. 2016 Nov 15:419(2):217-228. doi: 10.1016/j.ydbio.2016.09.012. Epub 2016 Sep 12     [PubMed PMID: 27634570]


Ishak MF, Chua KH, Asma A, Saim L, Aminuddin BS, Ruszymah BH, Goh BS. Stem cell genes are poorly expressed in chondrocytes from microtic cartilage. International journal of pediatric otorhinolaryngology. 2011 Jun:75(6):835-40. doi: 10.1016/j.ijporl.2011.03.021. Epub 2011 May 4     [PubMed PMID: 21543123]

Level 2 (mid-level) evidence


Rigueur D, Roberts RR, Bobzin L, Merrill AE. A requirement for Fgfr2 in middle ear development. Genesis (New York, N.Y. : 2000). 2019 Jan:57(1):e23252. doi: 10.1002/dvg.23252. Epub 2018 Oct 4     [PubMed PMID: 30253032]


Alvarez Y, Alonso MT, Vendrell V, Zelarayan LC, Chamero P, Theil T, Bösl MR, Kato S, Maconochie M, Riethmacher D, Schimmang T. Requirements for FGF3 and FGF10 during inner ear formation. Development (Cambridge, England). 2003 Dec:130(25):6329-38     [PubMed PMID: 14623822]

Level 3 (low-level) evidence


Hirokawa N, Takemura R. Biochemical and molecular characterization of diseases linked to motor proteins. Trends in biochemical sciences. 2003 Oct:28(10):558-65     [PubMed PMID: 14559185]

Level 3 (low-level) evidence


Silva AP, Blasca WQ, Lauris JR, Oliveira JR. Correlation between the characteristics of resonance and aging of the external ear. CoDAS. 2014 Mar-Apr:26(2):112-6     [PubMed PMID: 24918503]

Level 2 (mid-level) evidence


Mason MJ. Structure and function of the mammalian middle ear. II: Inferring function from structure. Journal of anatomy. 2016 Feb:228(2):300-12. doi: 10.1111/joa.12316. Epub 2015 Jun 23     [PubMed PMID: 26100915]


Ekdale EG. Form and function of the mammalian inner ear. Journal of anatomy. 2016 Feb:228(2):324-37. doi: 10.1111/joa.12308. Epub 2015 Apr 25     [PubMed PMID: 25911945]


Sennaroglu L. Histopathology of inner ear malformations: Do we have enough evidence to explain pathophysiology? Cochlear implants international. 2016:17(1):3-20. doi: 10.1179/1754762815Y.0000000016. Epub 2015 Jul 9     [PubMed PMID: 26158591]


Shibazaki-Yorozuya R, Nagata S. Preferential Associated Malformation in Patients With Anotia and Microtia. The Journal of craniofacial surgery. 2019 Jan:30(1):66-70. doi: 10.1097/SCS.0000000000004915. Epub     [PubMed PMID: 30616309]


Morita Y, Yamamoto Y, Oshima S, Takahashi K, Takahashi S. Pediatric middle ear cholesteatoma: the comparative study of congenital cholesteatoma and acquired cholesteatoma. European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery. 2016 May:273(5):1155-60. doi: 10.1007/s00405-015-3679-5. Epub 2015 Jun 5     [PubMed PMID: 26044405]

Level 2 (mid-level) evidence


Richter GT, Lee KH. Contemporary assessment and management of congenital cholesteatoma. Current opinion in otolaryngology & head and neck surgery. 2009 Oct:17(5):339-45. doi: 10.1097/MOO.0b013e3283303688. Epub     [PubMed PMID: 19745736]

Level 3 (low-level) evidence