According to Broda Barnes, MD:
"Shake the thermometer down before going to bed and leave it close by and within reach. As soon as you wake up, with a minimum of movement, put the thermometer in your armpit, next to the skin, and leave it in place for ten minutes. Record the reading for three to five consecutive days. Women who still have their menstrual period should not test on days 1,2,3, or 4 of their period, but can begin on day 5. Men, and girls and women who are not menstruating can test any time of the month."
Axillary (under the armpit) temperature taking was something that Barnes used to differentiate himself from the medical profession. Many other allopathic and alternative medical professionals and nutritionists do not feel it is necessary and it makes temperature taking more of a chore than it should be. However in a cool environment, the temperature of the extremities is sometimes a better indicator that the oral (or eardrum) temperature.
Temperatures consistently below 98.5 F may* indicate low thyroid function.
It's important to note that basal body temperature is influenced by many things besides thyroid. The resting heart rate will help to interpret the temperature. These numbers along with other indicators of thyroid function can be useful, but they have to be interpreted in relation to the entire physiological state. These indicators can serve as pieces to a larger puzzle.
* This information is not presented to take the place of a medical consult and is not meant for diagnosis.