This paper presents Natural Phonology as a functional theory. Natural Phonology is shown to be functional in two senses: as focusing on explanation and thus increasing our understanding of how language works, and as having practical applications, especially to second language acquisition and speech therapy. The contribution argues that crucial as formalism is in computational linguistics and speech technology, Natural Phonology, with less rigid and less formalized claims, has important applications in the areas where language and not totally predictable human factors are involved. The paper discusses approaches to autonomy in language, explanation and hypothesis in Natural Phonology, and applications of Natural Phonology.