Background: Over the last decade, annual incidence rates for thyroid cancer have been among the highest of all cancers in the Western world. However, the genomic mechanisms impacting thyroid carcinogenesis remain elusive. Methods: We employed an established mouse model of follicular thyroid cancer (FTC) with a homozygous proline to valine mutation ( Thrb PV/PV ) in the thyroid receptor β1 (TRβ1) and applied quantitative three-dimensional (3D) telomere analysis to determine 3D telomeric profiles in Thrb PV / PV , Thrb PV/ + , and Thrb +/+ mouse thyrocytes before and after histological presentation of FTC. Results: Using quantitative fluorescent in situ hybridization (Q-FISH) and TeloView™ image analysis, we found altered telomeric signatures specifically in mutant mouse thyrocytes. As early as 1 month of age, Thrb PV/PV mouse thyrocytes showed more telomeres than normal and heterozygous age-matched counterparts. Importantly, at the very early age of 1 month, 3D telomeric profiles of Thrb PV/PV thyrocyte nuclei reveal genetic heterogeneity with several nuclei populations exhibiting different telomere numbers, suggestive of various degrees of aneuploidy within the same animal. This was detected exclusively in Thrb PV/PV mice well before the presentation of histological signs of thyroid carcinoma. Conclusions: We identified quantitative 3D telomere analysis as a novel tool for early detection and monitoring of thyrocyte chromosomal (in)stability. This technique has the potential to identify human patients at risk for developing thyroid carcinoma.