Thyroid hormone (T3) regulates the function of many tissues within the body. The effects of T3 have largely been attributed to the modulation of thyroid hormone receptor-dependent gene transcription. However, nongenomic actions of T3 via the initiation of signaling events are emerging in a number of cell types. This study investigated the ability of short-term T3 treatment to phosphorylate and, therefore, activate signaling proteins in rat tissues in vivo. The kinases investigated included p38, AMP-activated protein kinase (AMPK), and extracellular signal-regulated kinase (ERK) 1/2. Following 2 h of T3 treatment, p38 and AMPK phosphorylation was increased in both the slow-twitch soleus and the fast-twitch plantaris muscles. In contrast, ERK1/2 was not activated in either muscle type. Neither p38 nor AMPK was affected in heart. However, AMPK activation was decreased by T3 in liver. ERK1/2 activation was decreased by T3 in heart, but increased in liver. Possible downstream consequences of T3-induced kinase phosphorylation were investigated by measuring cAMP response element binding protein (CREB) and thyroid hormone receptor DNA binding, as well as peroxisome proliferator-activated receptor-α coactivator-1 mRNA levels. Protein DNA binding to the cAMP or thyroid hormone response elements was unaltered by T3. However, peroxisome proliferator-activated receptor-α coactivator-1 mRNA expression was increased following 12 h of T3 treatment in soleus. These data are the first to characterize the effects of T3 treatment on kinase phosphorylation in vivo. We show that T3 rapidly modifies kinase activity in a tissue-specific fashion. Moreover, the T3-induced phosphorylation of p38 and AMPK in both slow- and fast-twitch skeletal muscles suggests that these events may be important in mediating hormone-induced increases in mitochondrial biogenesis in skeletal muscle.