Intonation is the phonologically structured variation in phonetic features, primarily pitch, to express phrase-level meanings. As in other speech sound domains, analyzing intonation involves mapping continuously variable physical parameters to categories. The categories of intonation are organized in a set of relations and rule-governed distributions that define the intonation system of a language. From physical realizations, as shown by pitch tracks, surface or phonetic tonal patterns can be identified in terms of tonal targets. Whether surface patterns correspond or not to categories within a given intonation system requires looking at their distributions and contrastiveness. In this paper, I assume the view that a transcription is an analysis of the intonation system, which ultimately aims to identify the contrastive intonation categories of a given language and establish how they signal meaning. Under this view, it is crucial to discuss the ways surface pitch patterns and structural pitch patterns (or phonological categories) are related. Given that intonational analysis is driven by system-internal considerations and that cues to a given category can vary across languages, it is also important to address the issue of how a language-specific transcription can be reconciled with the need and ability to do cross-language comparison of intonation. Bearing on these two issues, I discuss surface and structure in intonational analysis, drawing on mismatches between (dis)similarities in the phonetics and phonology of pitch contours, across languages and language varieties.