Background and Objectives: Amiodarone (AM), one of the most commonly prescribed antiarrhythmics, is frequently associated with thyroid dysfunction. Green tea extract (GTE) supplementation would attenuate oxidative stress and activate progenitor cells. However, the potential toxicity of GTE on various organs when administered at high doses has not been completely investigated. The present study aimed at investigating the possible relation between endogenous stem cells and GTE in overconsumption and AM induced thyroid damage in albino rat. Methods and Results: Twenty four male albino rats were divided into control group, GTE group (rats given 50 mg/kg), Overconsumption group (rats given 1,000 mg/kg GTE), AM group (rats given 30 mg/kg) and combined AM, GTE therapy group. AM and GTE were administered orally 5 days/week for 8 weeks. Serological tests were performed. Thyroid sections were exposed to histological, immunohistochemical and morphometric studies. In overconsumption group, multiple distorted follicles with cellular debris in the lumen and multiple follicles devoid of colloid were found. In AM group, multiple follicles exhibiting crescent of colloid and few follicles devoid of colloid were detected. In combined therapy group, multiple follicles were filled with colloid. Significant decrease in area of colloid and significant increase in the area% of collagen were recorded in overconsumption and AM groups. Area% of CD 105 +ve cells denoted significant increase in combined therapy group. Serological tests were confirmative. Conclusions: Endogenous SCs activation was proved in AM and GTE combined therapy group with regression of AM induced morphological, morphometric and serological changes. However, overconsumption of GTE recruited endogenous SCs suppression.