The role of thyroid hormone (TH) during fish larval development is well recognized particularly for flatfish as the common sole (Solea solea), while the consequences of thyroid homeostasis disruption during the larval-juvenile transitions are indistinct. To investigate these impacts, common sole newly hatched larvae were reared (triplicate) in four groups: the control group, the second is water-treated thyroxine (10 nM), the third and fourth groups were two doses goitrogen (perchlorate 30 and 100mg/L) for 30 days. By the end of exposure period, larval growth, survival, and whole body T4 and T3 were measured. In addition, thyroid follicles, intestine (intestinal fold height and goblet cell count) and liver were histologically examined. Exogenous Thyroxine significantly increased larval total length and number of goblet cells, and displayed larger thyroid follicles with more vacuoles, in addition to an increase in lipid accumulating hepatocytes. For goitrogen-treated fish groups, total weight, total length and survival significantly decreased and the 30 mg/L dose had more suppressive effect. The whole body T4 displayed significant decrease only for the goitrogen high dose, while no change was detected in the T3 content between treatments. Thyrocyte hypertrophy was observed in goitrogen-treated larvae groups and hepatocytes showed less lipid storage. Moreover, vacuoles between hepatocytes were detected for the high dose of goitrogen. These observations confirm the previously reported role of the TH in flatfish larvae development and growth. Moreover, the development and maintenance of both intestinal and hepatic tasks involve an intact thyroid endocrine axis.