Vapor phase ethyl tertiary butyl ether synthesis was investigated using heat treated heteropoly acid catalysts, namely silicotungtsic acid (STA) and tungstophosphoric acid-Keggin (TPA-K) and these results were compared with the results obtained with untreated catalysts. ETBE synthesis experiments showed that heat treatment of TPA-K at temperatures over 473 K had caused significant decrease of its catalytic activity. Activity of STA was more stable and deactivation of this catalyst was observed by heat treatment at 673 K and above. Heat treatment at high temperatures caused loss of constitutional water of STA and TPA-K, causing loss of protons, consequently the loss of acidity of the catalysts, resulting deactivation. FT-IR, TGA–DTA and DRIFTS analyses on pyridine-adsorbed catalysts supported the conclusions related to structural changes of STA and TPA-K with heat treatment. Highest ETBE yields were obtained at around 368 K, while at temperatures over 423 K formation of DEE and ethylene were observed due to dehydration of ethanol.