Thyroid cancer is the most prevalent endocrine cancer, and the prognosis depends on the type and stage of cancer at the time of discovery. The treatment involves (hemi-)thyroidectomy, possibly followed by additional therapeutic options. After treatment, patients are monitored using serum concentrations of endocrine tumour markers: thyroglobulin (Tg) in case of differentiated cancer and calcitonin in case of medullary thyroid cancer. Measuring Tg and calcitonin concentrations in serum may be challenging. In this review, we provide a complete overview of the evolution in laboratory measurements of Tg and calcitonin, with an emphasis on (pre-)analytical challenges and potential approaches to overcome current pitfalls.