Rare diseases · Sign or symptom
Micropenis
Short penis
HP:0000054
What it means
Abnormally small penis. At birth, the normal penis is about 3 cm (stretched length from pubic tubercle to tip of penis) with micropenis less than 2.0-2.5 cm.
Rare diseases that can present with this94
Very common80–99%
22- 46,XY difference of sex development due to isolated 17,20-lyase deficiency
- 46,XY ovotesticular difference of sex development
- 46,XY partial gonadal dysgenesis
- 49,XXXYY syndrome
- Branchioskeletogenital syndrome
- CHARGE syndrome
- Congenital fibrinogen deficiency
- Craniosynostosis-hydrocephalus-Arnold-Chiari malformation type I-radioulnar synostosis syndrome
- Diabetic embryopathy
- Diethylstilbestrol syndrome
- Hypogonadotropic hypogonadism-severe microcephaly-sensorineural hearing loss-dysmorphism syndrome
- Kallmann syndrome
- Leydig cell hypoplasia
- MEHMO syndrome
- Microcephaly-seizures-intellectual disability-heart disease syndrome
- MORM syndrome
- Normosmic congenital hypogonadotropic hypogonadism
- Paternal uniparental disomy of chromosome X syndrome
- Progeria-short stature-pigmented nevi syndrome
- Testicular agenesis
- Tetragametic chimerism syndrome
- Woodhouse-Sakati syndrome
Common30–79%
17- 45,X/46,XY mixed gonadal dysgenesis
- Cardiocranial syndrome, Pfeiffer type
- Distal deletion 15q syndrome
- Emanuel syndrome
- Intellectual disability-balding-patella luxation-acromicria syndrome
- Kallmann syndrome-heart disease syndrome
- Monosomy 18q syndrome
- Müllerian derivatives-lymphangiectasia-polydactyly syndrome
- Potocki-Shaffer syndrome
- Ring chromosome 13 syndrome
- SCARF syndrome
- STT3A-CDG
- STT3B-CDG
- Trisomy 8p syndrome
- X-linked intellectual disability, Nascimento type
- X-linked myotubular myopathy-abnormal genitalia syndrome
- Yunis-Varon syndrome
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. A sign on this page is a conversation to have with a clinician, not a conclusion.
Part of the broader category
Also called: Small penis
Tracking symptoms like this for someone? Eleplan keeps symptoms, diagnoses, medications and every specialist in one plan.
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.