Some conditions known to cause hypotonia include:

Congenital - i.e. disease a person is born with

Hypotonia, commonly known as floppy baby syndrome, is a state of low muscle tone (the amount of tension or resistance to stretch in a muscle), often involving reduced muscle strength. Hypotonia is not a specific medical disorder, but a potential manifestation of many different diseases and disorders that affect motor nerve control by the brain or muscle strength. Hypotonia is resistance to passive movement, whereas muscle weakness results in impaired active movement. Central hypotonia originates from the central nervous system, while peripheral hypotonia is related to problems within the spinal cord, peripheral nerves and/or skeletal muscles. Recognizing hypotonia, even in early infancy, is usually relatively straightforward, but diagnosing the underlying cause can be difficult and often unsuccessful. The long-term effects of hypotonia on a child's development and later life depend primarily on the severity of the muscle weakness and the nature of the cause. Some disorders have a specific treatment but the principal treatment for most hypotonia of idiopathic or neurologic cause is physical therapy, occupational therapy for remediation, and/or music therapy.

Hypotonia is thought to be associated with the disruption of input from stretch receptors and/or lack of the cerebellum’s facilitatory efferent influence on the fusimotor system, the system that innervates intrafusal muscle fibers thereby controlling muscle spindle sensitivity. On examination a diminished resistance to passive movement will be noted and muscles may feel abnormally soft and limp on palpation. Diminished deep tendon reflexes also may be noted. Hypotonia is a condition that can be helped with early intervention.

The prevalence rate has been estimated to be less than 1/1,000,000 worldwide. However, it is much more common in the French-Canadian population of the Saguenay and Lac-St-Jean regions of Quebec, Canada, where it has a frequency of about 1 in 2100 in live births, and a carrier rate of 1 in 23.

Dysdiadochokinesia, dysdiadochokinesis, dysdiadokokinesia, dysdiadokokinesis (from Greek "δυς" "dys" "bad", "διάδοχος" "diadochos" "succeeding", "κίνησις" "kinesis" "movement"), often abbreviated as DDK, is the medical term for an impaired ability to perform rapid, alternating movements (i.e., diadochokinesia). Complete inability is called adiadochokinesia.

The prognosis is poor. Patients are usually wheelchair bound by their 20s and die by their 30s.

Dysdiadochokinesia is a feature of cerebellar ataxia and may be the result of lesions to either the cerebellar hemispheres or the frontal lobe (of the cerebrum), it can also be a combination of both. It is thought to be caused by the inability to switch on and switch off antagonising muscle groups in a coordinated fashion due to hypotonia, secondary to the central lesion.

Dysdiadochokinesia is also seen in Friedreich's ataxia and multiple sclerosis, as a cerebellar symptom (including ataxia, intention tremor and dysarthria). It is also a feature of ataxic dysarthria. Dysdiadochokinesia often presents in motor speech disorders (dysarthria), therefore testing for dysdiadochokinesia can be used for a differential diagnosis.

Dysdiadochokinesia has been linked to a mutation in "SLC18A2", which encodes vesicular monoamine transporter 2 (VMAT2).

The prognosis is very poor. Two studies reported typical age of deaths in infancy or early childhood, with the first reporting a median age of death of 2.6 for boys and less than 1 month for girls.

The syndrome primarily affects young males. Preliminary studies suggest that prevalence may be 1.8 per 10,000 live male births. 50% of those affected do not live beyond 25 years of age, with deaths attributed to the impaired immune function.

Flaccid dysarthria is caused when damage occurs to the motor unit (one or more cranial or spinal nerves). Processes that can cause this include:

- Congenital disorders

- Demyelinating disorders

- Infectious/Inflammatory

- Degenerative disorders

- Metabolic

- Neoplastic

- Traumatic

- Vascular Diseases

- Flaccid Paralysis

Treatment of Ramsay Hunt Syndrome Type 1 is specific to individual symptoms. Myoclonus and seizures may be treated with drugs like valproate.

Some have described this condition as difficult to characterize.

SUCLA2 and RRM2B related forms result in deformities to the brain. A 2007 study based on 12 cases from the Faroe Islands (where there is a relatively high incidence due to a founder effect) suggested that the outcome is often poor with early lethality. More recent studies (2015) with 50 people with SUCLA2 mutations, with range of 16 different mutations, show a high variability in outcomes with a number of people surviving into adulthood (median survival was 20 years. There is significant evidence (p = 0.020) that people with missense mutations have longer survival rates, which might mean that some of the resulting protein has some residual enzyme activity.

RRM2B mutations have been reported in 16 infants with severe encephalomyopathic MDS that is associated with early-onset (neonatal or infantile), multi-organ presentation, and mortality during infancy.

Guanidinoacetate methyltransferase deficiency, also called GAMT deficiency, is an autosomal recessive metabolic disorder that primarily affects the nervous system and muscles. It is the first observed disorder of creatine metabolism.

Response to treatment is variable and the long-term and functional outcome is unknown. To provide a basis for improving the understanding of the epidemiology, genotype/phenotype correlation and outcome of these diseases their impact on the quality of life of patients, and for evaluating diagnostic and therapeutic strategies a patient registry was established by the noncommercial International Working Group on Neurotransmitter Related Disorders (iNTD).

The diagnosis of sepiapterin reductase deficiency in a patient at the age of 14 years was delayed by an earlier diagnosis of an initially unclassified form of methylmalonic aciduria at the age of 2. At that time the hypotonia and delayed development were not considered to be suggestive of a neurotransmitter defect. The clinically relevant diagnosis was only made following the onset of dystonia with diurnal variation, when the patient was a teenager. Variability in occurrence and severity of other symptoms of the condition, such as hypotonia, ataxia, tremors, spasticity, bulbar involvement, oculogyric crises, and cognitive impairment, is comparable with autosomal dominant GTPCH and tyrosine hydroxylase deficiency, which are both classified as forms of DOPA-responsive dystonia.

The TK2 related myopathic form results in muscle weakness, rapidly progresses, leading to respiratory failure and death within a few years of onset. The most common cause of death is pulmonary infection. Only a few people have survived to late childhood and adolescence.

Sepiapterin reductase deficiency is an inherited pediatric disorder characterized by movement problems, and most commonly displayed as a pattern of involuntary sustained muscle contractions known as dystonia. Symptoms are usually present within the first year of age, but diagnosis is delayed due to physicians lack of awareness and the specialized diagnostic procedures. Individuals with this disorder also have delayed motor skills development including sitting, crawling, and need assistance when walking. Additional symptoms of this disorder include intellectual disability, excessive sleeping, mood swings, and an abnormally small head size. SR deficiency is a very rare condition. The first case was diagnosed in 2001, and since then there have been approximately 30 reported cases. At this time, the condition seems to be treatable, but due to a lack of overall awareness and a series of atypical procedures used to diagnose this condition pose a dilemma.

Qazi–Markouizos syndrome is a rare hereditary condition characterized by non-progressive, congenital hypotonia, severe intellectual disability, an increased proportion of type 2 muscle fibers, which additionally exhibited increased size, as well as dysharmonic skeletal maturation. To date, the molecular mechanism of Qazi–Markouizos syndrome, which is also known as Puerto Rican infant hypotonia syndrome, remains unknown.

Most common causes of lower motor neuron injuries are trauma to peripheral nerves that serve the axons – a virus that selectively attacks ventral horn cells.

Disuse atrophy of the muscle occurs i.e., shrinkage of muscle fibre finally replaced by fibrous tissue (fibrous muscle)

Other causes include Guillain–Barré syndrome, "C. botulism", polio, and cauda equina syndrome; another common cause of lower motor neuron degeneration is amyotrophic lateral sclerosis.

Flaccid dysarthria is a motor speech disorder resulting from damage to peripheral nervous system (cranial or spinal nerves) or lower motor neuron system. Depending on which nerves are damaged, flaccid dysarthria affects respiration, phonation, resonance, and articulation. It also causes weakness, hypotonia (low-muscle tone), and diminished reflexes., Perceptual effects of flaccid dysarthria can include hypernasality, imprecise consonant productions, breathiness of voice, and affected nasal emission.

M2DS is one of the several types of X-linked intellectual disability. The cause of M2DS is a duplication of the MECP2 or Methyl CpG binding protein 2 gene located on the X chromosome (Xq28). The MeCP2 protein plays a pivotal role in regulating brain function. Increased levels of MECP2 protein results in abnormal neural function and impaired immune system. Mutations in the MECP2 gene are also commonly associated with Rett syndrome in females. Advances in genetic testing and more widespread use of Array Comparative Genomic Hybridization has led to increased diagnosis of MECP2 duplication syndrome. It is thought to represent ~1% of X-linked male mental disability cases.

The treatment of 2-Hydroxyglutaric aciduria is based on seizure control, the prognosis depends on how severe the condition is.

Micro syndrome also known as WARBM, and Warburg–Sjo–Fledelius syndrome, is a rare autosomal recessive genetic disorder characterized by microcephaly, microcornea, congenital cataract, intellectual or developmental disability, optic atrophy, and hypogenitalism.

RHS type 1 is caused by the impairment of a regulatory mechanism between cerebellar and brainstem nuclei and has been associated with a wide range of diseases, including Lafora disease, dentatorubropallidoluysian atrophy, and celiac disease.

There is no specific treatment for micro syndrome, but there are ways to help the disorders, and illnesses that come with it. Many individuals with Micro Syndrome need permanent assistance from their disorders and inabilities to move and support themselves. Seizures are not uncommon and patients should get therapy to help control them, and many patients also require wheelchairs to move, so an assistant would be needed at all times.

Those with micro syndrome are born appearing normal. At the age of one, mental and physical delays become apparent, along with some limb spasms. By the age of eight micro syndrome has already set in, and the patient will have joint contractures, Ocular Atrophy will become noticeable, the patient will most likely lose ability to walk, speak, and sometimes move at all.

The cause of this condition is apparently due to mutation in the UBE3B gene and is inherited via autosomal recessive manner. This gene is located at molecular location- base pairs 109,477,410 to 109,543,628 and position 24.11 on chromosome 12.