In this article, we discuss the relationship between instrumental and perceptual phonetic analyses. Using data drawn from typical and atypical speech production, we argue that the use of two-tier transcriptions, which can compare and contrast perceptual and instrumental information, is valuable both for our general understanding of the mechanisms of speech production and perception and also for assessment and intervention for individuals with atypical speech production. The central tenet of our case is that instrumental and perceptual analyses are not in competition to give a single "correct" account of speech data. They take instead perspectives on complementary phonetic domains, which interlock in the speech chain to encompass production, transmission and perception. (Contains 5 figures.)