Seed Rotation and Estrogen’s Impact on the Thyroid


This is one of my favorite techniques in rebalancing hormones – it is so simple, inexpensive and uninvasive. Yet, it produces surprising benefits and relief. The technique is called “seed rotation,” and can be used to boost estrogen levels in the first part of our cycle and progesterone levels in the second part.

Who is this for?

This technique can be used by anyone who is experiencing symptoms of estrogen dominance: irregular periods, heavy flows, substantial PMS, fibroids, endometriosis and even women going through peri-menopause and menopause. Estrogen dominance is also the leading cause of thyroid nodules and thyroid cancers.

The technique described here is based on a 30-day cycle, though most women’s cycles tend to run between 25 and 36 days. Only 10 to 15% of women have cycles that are exactly 28 to 30 days. Day 1 is counted as the first day of a period.

However, the seed rotation diet can also be used by women going through peri- and menopause.

As an example, this article is based on a 30-day cycle.

Which seeds should be used in what part of the cycle?

From Day 1 to Day 15 (or the middle of the cycle), we need more estrogen in order to build up our endometrium (uterus lining). This is called the follicular phase. Seeds such as flaxseed and pumpkin seeds, one tablespoon each per daycan naturally increase your estrogen levels.

From Day 15 to Day 30, or the second part of the cycle (also known as the luteal phase), the corpus luteum begins to release progesterone. This sex hormone will help thicken the uterus lining and prepare it for implantation. By adding one tablespoon of sesame seeds and one tablespoon of sunflower seeds per day in the luteal phase, we can naturally support the body to produce more progesterone, a sex hormone of which many women experience low levels.

Women going through peri- and menopause can start any time and follow the 2-week cycle.

The high contents of zinc in sesame seeds and vitamin E in sunflower seeds have been shown to stimulate progesterone production (see references below). By adding two tablespoons of sesame and sunflower seeds per day in the luteal phase, we can naturally support the body to produce more progesterone, a sex hormone of which many women experience low levels.

Feel free to download the Seed Rotation Guide that illustrates this method.


What does a balanced cycle look like?

Of course, being regular is one important factor, but there is much more to a balanced cycle beyond that. So many of us are accustomed to feeling terrible before our period (and some women in the mid-cycle or during ovulation as well) that we assume it is normal. It is not.

High estrogen (or estrogen metabolites) can be the cause of tender breasts, mood swings, hair loss, weight gain (especially around the tights and hips) , fibroids, endometriosis, breast and ovarian cysts, and even breast and ovarian cancer.

Low progesterone levels can manifest in ways similar to the above, along with feeling anxious, not being able to fall or stay asleep, infertility, miscarriages and menstrual headaches.

Rebalancing your cycle using a simple food-based technique like seed rotation can help alleviate many of the symptoms in as little as one or two months.

In a perfectly healthy woman, the menstrual cycle and the estrogen/progesterone production will happen naturally with no help or intervention. This is, unfortunately, not the case for many women today. Excessive stress leading to excessive cortisol release, environmental toxins, poor diet, food sensitivities, digestive issues, and high coffee or alcohol consumption can all contribute to irregular or painful periods, and even infertility.

Supporting the body with food that will help produce sufficient amounts of estrogen and progesterone is not only easy and cheap, but also non-invasive. This is why this form of healing is preferred by practitioners who work with food as medicine – this method simply works, while still being gentle on the body.

How estrogen dominance makes thyroid conditions worse?

It’s very seldom that a woman experiences one hormonal imbalance only. In the case of hypothyroidism and Hashimoto’s, I often see these combination:

  • hypothyroidism and estrogen dominance
  • hypothyroidism and adrenal fatigue
  • hypothyroidism and menopause (low estrogen)
  • hypothyroidism and PCOS (high blood sugar levels and/or high testosterone)

Since this article is about estrogen dominance, let’s take a look how excessive estrogen (or high levels of the harmful estrogenic metabolites) effect the thyroid:

  1. Estrogen dominance can be the cause of thyroid nodules and even thyroid cancer
  2. Excessive estrogen can cause an increase in the Thyroid Binding Globulin, the latter binds the thyroid hormone, making less of it available for the body to utilize. This will worsen the symptoms of hypothyroidism.

The seed rotation method can be an easy and inexpensive way of rebalancing your estrogen levels (see the above note on the 2:16 hydroxy-estrone ratio).

Why add more estrogens to our diet?

Many women worry that they are already experiencing estrogen dominance, so why add more estrogen in the form of phytoestrogens, such as flaxseed?

For this to be fully understood, we first need to establish that not all estrogens are “bad,” and the one that tends to be high in estrogen-dominant women is estradiol, also known as E2. Excessive levels of E2 have been linked to breast and prostate cancer. Flaxseed does not only suppress estradiol production, but it also nudges estradiol metabolism in a positive direction by generating a higher ratio of the protective metabolite 2-hydroxy-estrone versus the more harmful 16-hydroxy-estrone.


Related links: This week: “How to Use Food to Rebalance Hormones” – FREE Online Workshop, Register Here. 

Click Here To Join My FREE Online Workshop - Cooking For Balance


Easy ways of adding seed rotation to your diet

The easiest way to incorporate the seed combinations is by adding either two tablespoons of one seed or one tablespoon each of two different seeds to smoothies, salads or soups.

Another way to ensure regular seed consumption is by making your own seed crackers. They can easily be baked in a regular oven or prepared with a dehydrator.

RECIPE: Estrogen-boosting crackers [oven method]


Two tablespoons of flaxseed or pumpkin seeds per day have shown to help boost estrogen production. Pumpkin seeds are also known to be phytoestrogenic.

This can be equally valuable for menstruating women in the first part of the cycle (day 1 to 15, refer to the chart) as well as women going through peri- and menopause who would benefit from an estrogen boost.

This recipe is using an oven. If you have a dehydrator, feel free too use it and set it to 115F for 8 hours.

Estrogen Boosting Crackers
Equipment: thermometer, parchment paper and 18’ x 13’ baking tray
Serves: 20
  • 1 cup almonds
  • 1 cup flaxseed
  • 1 cup pumpkin seeds
  • 1 cup dried apples, roughly chopped
  • 1 cup roasted coconut flakes
  • 1 tablespoon apple cider vinegar
  • 1 tablespoon curry powder
  • 1 teaspoon sea salt
How To Make
  1. Soak almonds for 12 hours.
  2. Soak flaxseed and pumpkin seeds in 3 cups of water for 2 hours.
  3. Preheat the oven to 150F or the lowest temperature your oven allows. The trick to keeping the temperature low (ideally in the range of 120 to 150F) is to leave the oven door ajar. This will prevent the crackers from burning and will create air circulation to dry the crackers.
  4. Strain all the excess water from the almonds and combine with all the remaining ingredients. Toss to mix them well.
  5. Line the baking tray with parchment paper and spread the mixture evenly.
  6. Bake for 6 hours or until fully dried. It’s recommended to check your crackers regularly using the thermometer to be sure they are getting dried but not burned. If the oven gets too hot, just open the oven door slightly wider. I use a metal tool (like a can opener) to keep the oven door ajar. The second batch will be easier to make as you will know how to keep the oven temperature in the 120-150F range.
  7. These crackers store well for two weeks in an air-tight container.
Want more recipes?

Cooking for Balance WorkshopMedical References

“Zinc induced changes in the progesterone binding properties of the human endometrium,” European Society of Endocrinology

“Effect of dl-α-tocopherol acetate on progesterone metabolism,” Journal of Clinical Endocrinology & Metabolism

“Effect of dietary components, including lignans and phytoestrogens, on enterohepatic circulation and liver metabolism of estrogens and on sex hormone binding globulin (SHBG),” Journal of Steroid Biochemistry

“Effects of phytoestrogen extracts isolated from pumpkin seeds on estradiol production and ER/PR expression in breast cancer and trophoblast tumor cells,” Nutrition and Cancer, Taylor Francis Group.

“Phytoestrogens: the “natural” selective estrogen receptor modulators?” European Journal of Gynecology and Reproductive Biology

Thyroid Diet Starter Kit

Join the discussion 21 Comments

  • Alice says:

    This recipe is using an oven. If you have a dehydrator, feel free too use it and set it to 115F for 8 hours.

  • […] Nobody told me that being overly estrogenic can lead to breast cancer (I have a family history on my mother’s side), thyroid nodules (had three), and thyroid cancer. I wrote about it here. […]

  • Melanie Ann says:

    Thank you for this info! I missed two periods in a row, due to what I believe was binge eating out of control disruption as I know all our hormones go hand in hand. I’ve done much better this month stabilizing my blood sugar with healthy balanced meals every 3-4 hours. I also incorporated in 2 T of just pumpkin seeds (can’t do flax seeds pyroluric) the first 14 or maybe 15 days and then been doing 1 T sunflower seeds and 1 T sesame seeds since, now being Day 36 with no period. I realize re-establishing the rhythms of your body takes time, just wondering how long to wait and see if I get a period or to switch back to pumpkin seeds!?

  • Rita M says:

    What if you don’t have periods any more, will seeds still work?

    • Magdalena Wszelaki says:

      Depends on what you are suffering from. Seed rotation helps to rebalance estrogen and progesterone levels.

  • Wendy says:

    What do you mean by women who have gone through menopause to follow the 2-week cycle?

  • Lisa says:

    I’ve had endometrial ablation and no longer have periods. I do have my uterus and ovaries, I’m just not sure when my cycle would start since I’m not bleeding anymore. How can I figure out the best time to start this program? Can I just start whenever?

  • Anne says:

    Could this help with heavier than usual periods? I don’t know if I have hormone imbalance (will see doc soon) but my last 4 periods have been unusual — 2 heavier than usual with more clots, 1 spotting only, current period heavier and clotting again. I’m 40 and had a total thyroidectomy due to suspected cancerous nodules (benign) 7 months ago.

  • Angela says:

    HI Ann,
    Yes, it will help. Heavy periods and blood clots is typical estrogen
    dominance symptoms. Midcycle spotting is low progesterone.

  • Kathy says:

    I’ve felt my best during my 2 pregnancies and nursing periods. A few months after I stopped nursing my symptoms came back and even more severe. I tend to get cyclical migraines, vaginal yeast infection ( never had them before!!), and I catch a cold almost every 3 -4 weeks:(.. my immune system has basically weakened drastically.. I’ve had Mirena placed last year ( right after my second child) and that’s not helping either. I’m getting it removed. Do you think the seed diet would help?
    Any advice is much appreciated!!.

    • Julie McGinnis says:

      Hi, It is not uncommon for women to feel better when pregnant and nursing. Your symptoms sound like hormone imbalances and Magdalena’s Cooking for Balance Program could be of great benefit to your healing. The seed rotation can help with balancing hormones but the addition of healing foods for your migraines and yeast imbalance would be most beneficial. Here is the link to the program

  • Katie says:

    I have low progesterone, I always have a week of spotting before I start my actual period. It has been 6 years of infertility as well. How long does it take approximately for the seed rotation to effectively balance the hormones? Is the typically enough to bring about the balance?

  • Susana Rodrigues says:

    Hello, Can we grind the seeds? And if so, should we grind them when we are about to it it or we can grind them and keep them in a bottle and take the 2 tbsp every day?

    • Angela Sidlo says:

      Hi Susana,
      You can grind the flaxseed. If you can, grind it fresh everyday. The longer the ground seeds are exposed to the air the faster they lose their potency. I use the coffee grinder blade on my bullet blender to grind the flaxseed. The other seeds do not need to be ground. Just toss into your morning smoothie or sprinkle on salads or starry veggies.
      Angela HB Team

  • Ingrid says:

    I have low thyroid problems(conversion of t4 to t3), adrenal fatigue and problems with painfull periods and breast cysts. Since i am 50 year old, i never know if i have a estrogen dominance or not, as usually around this age estrogen declines, but the cysts seem to point to to much. Should i put more estrogens in my diet or not? I have also chronic lyme disease, but what is the main cause of the hormonal inbalance? The adrenals, the thyroid or the female hormones?

  • Elinor says:

    Hello, quick question, if I try the seed rotation, does it mean that during one rotation, the seeds from the other rotation must be avoided in order for the two indicated ground seed types to work properly? I often eat sunflower seeds as a quick snack on the go & wonder if it would mess things up if eaten during the non sunflower cycle. Also, what if I eat more than one tablespoon? Will that sets things off kilter? (I’ve a pumpkin seed & dandelion pesto recipe for instance)

    Thank you.

  • […] poziomu naturalnego estrogenu i progesteronu pod nazwą seed rotation diet (więcej informacji tutaj). Dieta ta jest bardzo prosta i polega na spożywaniu przez pierwszą połowę cyklu po 1 łyżce […]

Leave a Reply