T3 containing medications (such as desiccated thyroid or Cytomel) cause a peak in Free T3 levels a few hours after ingestion (42% within the first 4 hours), and then a decline until the next dose.  Even T4 medications like Synthroid or levothyroxine cause a small bump in thyroid levels a few hours after a dose (16% rise in Free T4 with no change in free T3). This peak and trough of the Free T3 level can greatly affect one’s lab results, depending on when the labs are drawn. As an example, I normally take my desiccated thyroid 4x/day, before breakfast, lunch, dinner, and bedtime, and then test in the morning around 9 a.m. This would result in a lower lab result than what I normally experience, because it is 9-10 hours from my last dose, while I normally dose closer to every 5-6 hours during a normal day. I also have no idea how high my Free T3 peaks, since I am measuring a trough. So if my labs showed me at top-of-range, my peak levels are probably significantly over range, and could be a cause for concern.
Thyroid labwork could also be done 5-6 hours after the last dose, to see where the Free T3 falls in the reference range. Depending on how often one doses, this should give a lab result between the peak and trough levels. Taking a lower dose more often will cause smaller peaks and troughs. All labs are only guidelines though, and symptoms should always trump labs when determining a dose.
Thyroid hormone levels, in excess, will affect other lab results. Total cholesterol may become quite low, while SHBG (sex hormone binding globulin), calcium, and alkaline phosphatase may become elevated. The last three markers correlate with hyperthyroidism and bone loss, and should not be ignored.  The hyperthyroid state (too much T3, not a low TSH) causes osteoporosis, which is why doctors are so wary of prescribing too much T3.  Cortisol, free testosterone and DHEA values may also fall below the reference range when too much thyroid hormone is taken.  This may explain why so many are told to take hydrocortisone and supplement sex hormones when on the T3-only protocol.
- P. Saravanan, H. Siddique, D. J. Simmons, R. Greenwood, C. M. Dayan. Twenty-four Hour Hormone Profiles of TSH, Free T3 and Free T4 in Hypothyroid Patients on Combined T3/T4 Therapy. Exp Clin Endocrinol Diabetes 2007; 115(4): 261-267. https://www.thieme-connect.com/ejournals/abstract/eced/doi/10.1055/s-2007-973071
- Ford HC, Crooke MJ, Murphy CE. Disturbances of calcium and magnesium metabolism occur in most hyperthyroid patients. Clin Biochem. 1989 Oct;22(5):373-6. http://www.ncbi.nlm.nih.gov/pubmed/2805340
- Steven R. Smith, Jennifer C. Lovejoy, George A. Bray, Jennifer Rood, Marlene M. Most, Donna H. Ryan. Triiodothyronine increases calcium loss in a bed rest antigravity model for space flight. Journal of Metabolism. Volume 57, Issue 12, Pages 1696-1703 (December 2008). http://www.metabolismjournal.com/article/S0026-0495%2808%2900283-7/abstract
- Skjöldebrand Sparre L, Kollind M, Carlström K. Ovarian ultrasound and ovarian and adrenal hormones before and after treatment for hyperthyroidism. Gynecol Obstet Invest. 2002;54(1):50-5. http://www.ncbi.nlm.nih.gov/pubmed/12297719