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干细胞是未分化细胞，能够自我更新和分化成一种或多种功能的细胞。“成体”干细胞，通常称为“祖细胞”，只能分化为它们所在的器官特异性的细胞型。一些器官有成体干细胞的存在，其在疾病或损伤后的修复中起着关键作用。虽然许多年前就假设甲状腺干/祖细胞的存在 [36] ，但近几年才在成人甲状腺中找到支持的证据。
首先在骨髓中发现一群叫侧群细胞（Side Population, SP）的亚群细胞，随后发现存在于各种非造血组织 [37] 。这些细胞的特征是可外排活性染料Hoechst33342，与真正的干细胞有许多相同的特征。SP细胞有助于肝实质的再生或骨骼肌管的形成。甲状腺中也发现SP细胞 [38] ；小鼠中，SP细胞大部分位于滤泡间隙中，少于甲状腺总细胞的1%。SP细胞表达干细胞标志物Oct-4和核干因子（Nucleostemin），而几乎检测不到分化标志物如甲状腺球蛋白（Tg）和甲状腺过氧化物酶（TPO）。此外，只有很少的SP细胞表达C细胞标志物——降钙素。人类结节性甲状腺肿的甲状腺细胞中已分离出SP细胞，并显示与小鼠SP细胞相似的分子特征 [39] 。通常，培养中的SP细胞会进行组织特异性分化。值得注意的是，从正常小鼠甲状腺分离的SP细胞在培养中保持未分化状态，并且不能排列成卵泡样结构。相反，人类SP细胞能够在体内增殖，具有甲状腺表型，对TSH应答。小鼠和人类SP细胞分别来源于正常和甲状腺肿组织，尚不清楚小鼠和人类SP细胞之间的差异是否取决于培养条件不同或细胞来源不同。
除了SP细胞，实性细胞巢（Solid Cell Nests, SCN）的主要细胞也显示许多干细胞的特征。在这些细胞中，不表达生成甲状腺球蛋白或降钙素的基因特异性，而表达端粒酶 [40] 和p63 [41] , p63是常在多层上皮细胞的基底/干细胞中检测到的转录因子。此外，SCN的主要细胞中BCL2的表达增加 [40] ，BCL2是在TFCs中持续表达的抗凋亡蛋白 [42] 。这种分子特征与干细胞的定义相符，提示SCN的主要细胞可能是分化为产生激素细胞的多能干细胞的来源。
人类TFCs更新缓慢，一生约分裂5次 [36] 。因此，人在出生后甲状腺表现为“休眠器官”。然而在动物模型中已经证明，甲状腺在受到严重干扰后（如严重的实验性甲状腺炎 [43] 或甲状腺部分切除术 [44] ）可再生和恢复滤泡结构。甲状腺部分切除术后，表达Sca 1（干细胞抗原1）的细胞在术后的几天内增殖 [45] ，该细胞位于甲状腺的非滤泡间质区。
以前的数据似乎表明，甲状腺的再生可能是甲状腺干/祖细胞替换被破坏的滤泡细胞池而增殖和分化的结果。然而，我们目前缺乏甲状腺干细胞存在的确凿证据，不知道这些细胞的生理学和病理学作用。
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