Difficulties Diagnosing Hypothyroidism

The thyroid is a small, butterfly-shaped gland located at the base of the neck, just below the Adam’s apple. The thyroid gland makes two main hormones: thyroxine (T-4) and triiodothyronine (T-3). Hypothyroidism happens when the thyroid gland doesn’t make enough hormones.  

In Marilyn Shannon’s book Fertility, Cycles and Nutrition, she lists signs of low thyroid function that can be seen on a woman’s chart:  

  • Unusually low basal temperatures (preovulatory temperatures around 97.3 °F. and lower) 
  • Heavy menses 
  • Prolonged menses 
  • Delayed ovulation 
  • Long or very long cycles 
  • Prolonged less fertile mucus 
  • Short luteal phase 
  • Anovulatory cycles 
  • Unexplained infertility 
  • Miscarriage 

When talking about low thyroid function, Shannon states,  

For reasons that are not always clear, however, low thyroid function may not be detected by blood tests for the various thyroid hormones. This problem of diagnosis has led to the term “subclinical hypothyroidism.” Or, you may have had a diagnosis of hypothyroidism and are taking thyroid medication, yet you are still experiencing cycle irregularities. Insufficient thyroid hormone replacement could be involved.” 

WHY AREN’T THYROID TESTS COMPLETELY RELIABLE? Shannon states there are several theories to explain why tests for thyroid function are not always accurate. First, the thyroid hormone in the blood is overwhelmingly the inactive T4 hormone, which must be converted in the tissues to the active form, T3. Direct testing of the active T3 hormone in each cell is not possible. The conversion of T4 to T3 depends on a number of nutrients, including the mineral selenium. Second, the standards for “normal” thyroid function may be too broad, even though the range for “normal” has been narrowed in the last few years. Third, high levels of estrogen can block thyroid function within the body cells, as can high levels of stress hormones.1  

Below is an interesting story Shannon related of a woman she worked with as a NFP coach and the woman’s experience with difficulties diagnosing hypothyroidism. 


A woman I’ll call Jane was very much helped by Dr. Barnes’ research2 regarding the value of the basal temperature chart, other charted information, her own persistence, and the assistance of an openminded medical doctor. When she contacted me, her preovulatory temperatures were as low as 96.3°F. Her temperature shift was poor, with only nine elevated temperatures in the luteal phase before the next menses. (Twelve to sixteen elevated temperatures are normal for the luteal phase.) She had brown bleeding at the end of the menstrual period, and then a pattern of less-fertile “tacky” mucus that began immediately and never changed to stretchy, more-fertile mucus. 

Jane was in her mid-30’s at the time and had four young children, none of them breastfeeding. She made some other notes on her charts, especially about the painful periods. She felt generally unwell and was avoiding a pregnancy. Because of the chart problems—this was her monthly pattern—the abstinence phase was prolonged. She said she had low libido and bad PMS. 

When I reviewed Jane’s charts, I felt sure that the problem was low thyroid function and suggested that she get her thyroid hormones tested. Jane did see her family doctor, who performed standard thyroid tests at her request. All came back normal. I encouraged her to seek further testing. She followed up by seeing a hormone specialist who performed new tests. All were normal. When Jane asked this doctor about a lump she found growing on the front of her neck, the specialist was not at all concerned about it. 

Jane persisted and made an appointment with a second specialist. When she met him, he had her test results from the previous doctors in his hand, and he said as he walked into the consultation room: “I’m not going to redo these tests. You’ve already been tested twice. I’m going to put you on [an anti-anxiety medication]. Ninety percent of the patients who come here are anxious.” When Jane called his attention to the lump on her neck, he completely changed. She left with an appointment for a biopsy of her thyroid gland and the fear that it might be cancer.  

At this point Jane decided to use the services of a more holistic medical doctor in another town. This doctor took her history, reviewed her NFP charts and her previous medical tests, and concluded that she had low thyroid function. He recommended that she first have the abnormal growth on her thyroid evaluated and removed by a surgeon. She did so; it turned out to be a benign hypothyroid goiter.  

Afterwards, the nutritionally-aware doctor prescribed supplements similar to those in (Fertility Cycles and Nutrition) to see if he could help her improve her thyroid function. (Jane had already tried the nutrition recommended in a previous edition of my book very conscientiously, but to no avail.) When nutrition failed to make a difference, the doctor started Jane on the natural Armour thyroid hormone. He very gradually increased her dose over a period of months.  

A year later, Jane was so pleased with her improvement that she surprised me by mailing me a recent NFP chart. While her preovulatory temperatures were still low compared to most women’s charts, they were noticeably higher than they had been. More significantly, her luteal phase, which had been only nine days long, was lengthened to twelve days, which is within the normal range. Her period was shorter and lighter, and her mucus pattern was very much improved and was completely normal. The time of abstinence the new chart required was far less than for her previous charts when her hypothyroidism was undiagnosed and untreated. 

In the above example, several things had to occur for her to have a positive outcome: recording of the basal temperature in her chart, other charted symptoms and information, the woman’s own persistence, and the assistance of an openminded medical doctor – the key probably being her tenacity and determination to get answers! 

Marilyn Shannon suggests that if your chart or symptoms fit those listed at the beginning of this article, make sure that you first improve your diet, and then begin taking a comprehensive multivitamin/multimineral, along with flax oil and/or fish oil. If you are very athletic, reduce your workouts until your cycles and health improve. Instead, try milder exercise in cool weather, or consider swimming to allow your body to experience lower temperatures, which may stimulate your thyroid function. If you are not able to resolve your symptoms, seek the assistance of a nutritionally oriented health professional.3 


  1. Shannon, M. Fertility, Cycles and Nutrition (Couple to Couple League, 2019, p. 152) 
  1. Barnes, Broda, M.D., Hypothyroidism: The Unsuspected Illness (HarperCollins Publishers, 1976) 
  1. Shannon, M. (2019, p. 154)