Thyroid and parathyroid diseases are fairly common and can be either hereditary or sporadic in nature. Tumors and tumor-like processes account for the majority of surgical pathology specimens in both of these endocrine organs. Molecular alterations are well known to occur in both the hereditary and the sporadic settings, and include alterations in tumor suppressor genes and oncogenes. The genetic pathways of tumors of parathyroid and thyroid are beginning to be well understood and are proving to be useful diagnostic, prognostic, and potential therapeutic targets. The molecular alterations in parathyroid and thyroid tumors and tumor-like processes are reviewed, with a focus on the potentially clinically useful diagnostic markers.