This is some of the info I found online.http://www.buzzle.com/articles/hypotonia-symptoms-causes-and-treatments.html

What causes Hypotonia?
Genetic disorders such as Krabbe disease, Werding-Hoffman disease, Aicardi syndrome, Down syndrome, Achondroplasia, canavan disease, Riley-Day syndrome (also known as Familial dysautonomia), Griscelli syndrome, Leigh disease, Marfan syndrome, Rett syndrome, Prader-Willi syndrome, Myotonic dystrophy, Menkes syndrome, centronuclear and myotubular myopathy, Dejerine sottas syndrome, Septo-optic dysplasia, Tay-Sachs disease, 22q13 deletion syndrome, Trisomy 13 and FG syndrome etc. are the main conditions that causes hypotonia in infants/children.

There are many conditions leading to development of hypotonia, which are: muscular dystrophy, metachromatic leukodystrophy, infectious disease such as encephalitis, sepsis, meningitis, infant botulism, Guillain-Barre syndrome, poliomyelitis etc., myasthenia gravis, celiac disease, problems caused due to improper vaccination or abnormal reaction to vaccination, congenital cerebellar ataxia, congenital hypothyroidism, hypotonic cerebral palsy, teratogenesis (caused from utero exposure to Benzodiazepines), sensory integration dysfunction, dyspraxia, metabolic disorders such as hypervitaminosis (vitamin poisoning or vitamin overdose), rickets and kernicterus, problems with central nervous system dysfunction, any kind of brain injury that had direct or indirect effect on the nervous system (brain injury caused in an accident or injury caused in a child suffering from shaken baby syndrome), motor neuron lesions etc.

How is Hypotonia diagnosed?
Physical examination can help in confirming some symptoms such as inability to flex muscles for longer time, delayed response to stimulations, delayed physical development, speech problems, feeding problem for an infant due to inability to suck breasts properly etc. If the disorder is thought to have affected brain then it is considered to be cerebral palsy, if the problem is related to muscles then it is called as muscular dystrophy.

Family medical history, CT scan, MRI scan, EEG (Electroencephalogram), genetic testing (which involve testing for abnormalities in genes, chromosome karyotyping etc.), blood test, electromyography muscle test, muscle and/or nerve biopsy, spinal taps (also known as lumbar puncture, used to collect cerebrospinal fluid for analysis) etc. are other tests used to diagnose Hypotonia disorder.

I think one of the tests was CPK or something like that. I don't know what else the doctor was looking for, but he didn't feel that any more testing was necessary, not even an MRI. My son's hypotonia is mild but he does not have the endurance that other kids have even though he gets regular exercise. We were told that he had hypotonia when he was 12 months old. He couldn't stand up without support and the muscles in his legs quivered like they were really weak but he was able to walk at 18 1/2 months. His core muscles and legs always seemed weaker than the rest of him. I have tried to learn as much as I could about all of this but I am still really confused also.