Rare diseases · Sign or symptom
Ambiguous genitalia
Ambiguous external genitalia
HP:0000062
What it means
A genital phenotype that is not clearly assignable to a single gender. Ambiguous genitalia can be evaluated using the Prader scale: Prader 0: Normal female external genitalia. Prader 1: Female external genitalia with clitoromegaly. Prader 2: Clitoromegaly with partial labial fusion forming a funnel-shaped urogenital sinus. Prader 3: Increased phallic enlargement. Complete labioscrotal fusion forming a urogenital sinus with a single opening. Prader 4: Complete scrotal fusion with urogenital opening at the base or on the shaft of the phallus. Prader 5: Normal male external genitalia. The diagnosis of ambiguous genitalia is made for Prader 1-4.
Note that this term can include or combine variations in size and shape, with partial or complete absence of structures. It is preferable to describe the individual components, which are defined below. It is nonetheless a widely used bundled term and as such is retained here. The distinction of this finding from a marked degree of Hypospadias is an example of how this term can be problematic. Genetic gender is determined at fertilization, whereby the presence of a Y chromosome determines male gender. Normally, genetic gender determines gonadal gender which in turn determines phenotypic gender. Testicular development is an active process requiring expression of the primary testis determining gene SRY, which is located on the Y chromosome.
Rare diseases that can present with this66
Very common80–99%
18- 46,XX ovotesticular difference of sex development
- 46,XX testicular difference of sex development
- 46,XY difference of sex development due to 17-beta-hydroxysteroid dehydrogenase 3 deficiency
- 46,XY difference of sex development due to 5-alpha-reductase 2 deficiency
- 46,XY ovotesticular difference of sex development
- 46,XY partial gonadal dysgenesis
- 49,XXXYY syndrome
- Bartsocas-Papas syndrome
- Congenital adrenal hyperplasia due to 11-beta-hydroxylase deficiency
- Leydig cell hypoplasia
- Meacham syndrome
- Penile agenesis
- Sirenomelia
- Sudden infant death-dysgenesis of the testes syndrome
- Testicular regression syndrome
- Tetragametic chimerism syndrome
- X-linked alpha-thalassemia-intellectual disability syndrome
- X-linked lissencephaly with abnormal genitalia
Common30–79%
25- 10q22.3q23.3microduplication syndrome
- 45,X/46,XY mixed gonadal dysgenesis
- Ablepharon macrostomia syndrome
- Beemer-Ertbruggen syndrome
- Campomelic dysplasia
- Cloverleaf skull-multiple congenital anomalies syndrome
- Fetal trimethadione syndrome
- Fraser syndrome
- Holoprosencephaly-postaxial polydactyly syndrome
- Isochromosomy Yp syndrome
- Isochromosomy Yq syndrome
- LUMBAR syndrome
- Maternal uniparental disomy of chromosome X syndrome
- Meckel syndrome
- Monosomy 9p syndrome
- Neu-Laxova syndrome
- PAGOD syndrome
- Partial androgen insensitivity syndrome
- Pelvis-shoulder dysplasia
- Pontocerebellar hypoplasia type 7
- Ring chromosome 13 syndrome
- Ring chromosome Y syndrome
- Short rib-polydactyly syndrome, Verma-Naumoff type
- Smith-Lemli-Opitz syndrome
- Testicular agenesis
Sometimes5–29%
20- Autosomal dominant omodysplasia
- Autosomal dominant popliteal pterygium syndrome
- Caudal regression syndrome
- Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency
- Congenital adrenal hyperplasia due to cytochrome P450 oxidoreductase deficiency
- Congenital osteogenesis imperfecta-microcephaly-cataracts syndrome
- Desmosterolosis
- Distal deletion 13q syndrome
and 12 more in this range
The range is how often this sign appears among people diagnosed with each disease — it is not a probability of having any of them. Many of these signs also occur in common, non-rare conditions, and Orphanet separately records 2 diseases where this sign is specifically absent. A sign on this page is a conversation to have with a clinician, not a conclusion.
Part of the broader category
Also called: Ambiguous external genitalia at birth · Intersex genitalia
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Start free with EleplanThis page uses the Human Phenotype Ontology (2026-06-23) — Human Phenotype Ontology Consortium, hpo.jax.org. Disease associations from Orphanet (INSERM), CC BY 4.0. Content is educational and is not medical advice.