disease a person is born with (including genetic disorders presenting within 6 months)

Genetic disorders are the most common cause
22q13 deletion syndrome a.k.a. Phelan–McDermid syndrome
3-Methylcrotonyl-CoA carboxylase deficiency
Achondroplasia
Aicardi syndrome
Autism spectrum disorders
Canavan disease
Centronuclear myopathy (including myotubular myopathy)
Central core disease
CHARGE syndrome
Cohen syndrome
Costello syndrome
Dejerine–Sottas disease (HMSN Type III)
Down syndrome a.k.a. trisomy 21 — most common
Ehlers–Danlos syndrome
Familial dysautonomia (Riley–Day syndrome)
FG syndrome
Fragile X syndrome
Griscelli syndrome Type 1  (Elejalde syndrome)
Holocarboxylase synthetase deficiency / Multiple carboxylase deficiency
Krabbe disease
Leighs disease
Lesch–Nyhan syndrome
Marfans syndrome
Menkes syndrome
Methylmalonic acidemia
Myotonic dystrophy
Niemann–Pick disease
Nonketotic hyperglycinemia (NKH) or Glycine encephalopathy (GCE)
Noonan syndrome
Neurofibromatosis
Patau syndrome a.k.a. trisomy 13
Pituitary dwarfism/growth hormone deficiency(in adults)
Prader–Willi syndrome
Rett syndrome
Septo-optic dysplasia (de Morsier syndrome)
Snyder–Robinson syndrome (SRS)
Spinal muscular atrophy (SMA)
Succinic semialdehyde dehydrogenase deficiency (SSADH)
Tay–Sachs disease
Werdnig–Hoffmann syndrome – Spinal muscular atrophy with congenital degeneration of anterior horns of spinal cord. Autosomal recessive 
Wiedemann–Steiner syndrome
Williams syndrome
Zellweger syndrome a.k.a. cerebrohepatorenal syndrome
Developmental disability
Cerebellar ataxia (congenital)
Sensory processing disorder
Developmental coordination disorder
Hypothyroidism (congenital)
Hypotonic cerebral palsy
Teratogenesis from in utero exposure to Benzodiazepines

Acquired
Acquired – i.e. onset occurs after birth

Genetic
Muscular dystrophy (including Myotonic dystrophy) – most common
Metachromatic leukodystrophy
Rett syndrome
Spinal muscular atrophy
Infections
Encephalitis
Guillain–Barré syndrome
Infant botulism
Meningitis
Poliomyelitis
Sepsis
Toxins
Infantile acrodynia (childhood mercury poisoning)
Autoimmunity disorders
Myasthenia gravis – most common
Abnormal vaccine reaction
Celiac disease
Metabolic disorder
Hypervitaminosis
Kernicterus
Rickets
Neurological
Traumatic brain injury, such as the damage that is caused by shaken baby syndrome
Lower motor neuron lesions
Upper motor neuron lesions
Miscellaneous
Central nervous system dysfunction, including cerebellar lesions and cerebral palsy
Hypothyroidism
Sandifer syndrome
Neonatal benzodiazepine withdrawal syndrome in children born to mothers treated in late pregnancy with benzodiazepine medications

Diagnosis
The approach to diagnosing the cause of hypotonia (as with all syndromes in neurology) is first localization.
Treatment
The outcome in any particular case of hypotonia depends largely on the nature of the underlying disease. In some cases, the underlying cause is treatable. But in general, treatment comprises providing supportive care with rehabilitation services, nutritional and respiratory support.Along with normal pediatric care, specialists who may be involved in the care of a child with hypotonia include developmental pediatricians (specialize in child development), neurologists, neonatologists (specialize in the care of newborns), geneticists, occupational therapists, physical therapists, speech therapists, orthopedists, pathologists (conduct and interpret biochemical tests and tissue analysis), and specialized nursing care. If the underlying cause is known, treatment is tailored to the specific disease, followed by symptomatic and supportive therapy for the hypotonia. In very severe cases, treatment may be primarily supportive, such as mechanical assistance with basic life functions like breathing and feeding, physical therapy to prevent muscle atrophy and maintain joint mobility, and measures to try to prevent opportunistic infections such as pneumonia. Treatments to improve neurological status might involve such things as medication for a seizure disorder, medicines or supplements to stabilize a metabolic disorder, or surgery to help relieve the pressure from hydrocephalus (increased fluid in the brain). The National Institute of Neurological Disorders and Stroke states that physical therapy can improve motor control and overall body strength in individuals with hypotonia. This is crucial to maintaining both static and dynamic postural stability, which is important since postural instability is a common problem in people with hypotonia.