The knowledgeable egreg gives advice about what packages to load when using Greek and a lot depends on how new the TeX distribution is:
http://tex.stackexchange.com/questions/122992/classic-thesis-lyx-language-problem Currently, LyX outputs this in the preamble for Greek: \documentclass[greek]{article} \usepackage[T1]{fontenc} \usepackage[iso-8859-7]{inputenc} \usepackage{babel} Is that correct? Scott
