Sleep has a great impact on the control of hormones, and hormones have a great impact on the control of sleep. In particular this article will visit the effects of sleep on the hypothalamic–pituitary–thyroid axis. If you are having problems with weight gain, temperature control, or energy levels then chances are the sleep deprivation is causing a chronic HPT axis imbalance.
An HPT axis imbalance due to sleep deprivation is not always because of polyphasic sleep but polyphasic sleep can exacerbate a previously dormant HPT problem (due to other bad lifestyle factors). Some factors could be bad current or previous diet, lack of previous exercise, genetics, or toxins. These factors will usually create sleep inefficiency (low total SWS / low total delta brain activity / density) which will in turn cause sleep deprivation. In these cases polyphasic sleep is not to blame, but the other factors do not allow the person to adapt to polyphasic sleep.
An HPT axis imbalance can be because of polyphasic sleep, like when someone gets too little total SWS or total delta brain activity: one case is low total sleep, going below a minimum threshold. This is the origin of the 3h total rule: when someone is not allowing for the minimum effective sleep total they are limiting their potential for total SWS and total REM. Even if they get a sleep ratio of 40% SWS and 40% REM (an incredible sleep efficiency) they may still be under that healthful threshold, and therefore negatively and chronically effecting their HPT axis.
How the HPT Axis works
The major portion of T3, however, is produced in peripheral organs, e.g. liver, adipose tissue, glia and skeletal muscle by deiodination from circulating T4. Deiodination is controlled by numerous hormones and nerval signals including TSH, vasopressin and catecholamines.
How the HPT Axis goes wrong
The average T4 decline during the last several days of the experimental period is 79 ~o below baseline. Plasma total triiodothyronine (TT3) also declines, but not as severely, to 52~o below baseline 
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