The atmospheres of extra-solar planets are small orbital distances are subject to intense UV radiation from their primary stars.Absorption of this radiation heat the atmosphere to high temperatures, alters the composition of the atmosphere from molecular species to atomic and ionic species and drives escape of the atmosphere.The high temperatures and low molecular weight cause greatly extended upper atmospheres that can be detected and studied in UV transit observations.The rapid escape of H and H+ drags along heavier species such as O+ and Si++, that can also be observed in transit measurements.This talk will briefly review the basic theory for these highly-irradiated planets, present some recent results on models for extra-solar upper atmospheres, and discuss the implications of upper atmosphere observations for the structure of the lower atmospheres of extra solar planets.