In this chapter, the authors examine the issue of digital formats for document encoding, archiving and publishing, through the specific example of “born-digital” scholarly journal articles. This small area of electronic publishing represents a microcosm of the state of the art, and provides a good basis for this discussion. The authors will begin by looking at the traditional workflow of journal editing and publication, and how these practices have made the transition into the online domain. They will examine the range of different file formats in which electronic articles are currently stored and published. They will argue strongly that, despite the prevalence of binary and proprietary formats such as PDF and MS Word, XML is a far superior encoding choice for journal articles. Next, the authors look at the range of XML document structures (DTDs, Schemas) which are in common use for encoding journal articles, and consider some of their strengths and weaknesses. The authors will suggest that, despite the existence of specialized schemas intended specifically for journal articles (such as NLM), and more broadly-used publication-oriented schemas such as DocBook, there are strong arguments in favour of developing a subset or customization of the Text Encoding Initiative (TEI) schema for the purpose of journal-article encoding; TEI is already in use in a number of journal publication projects, and the scale and precision of the TEI tagset makes it particularly appropriate for encoding scholarly articles. They will outline the document structure of a TEI-encoded journal article, and look in detail at suggested markup patterns for specific features of journal articles. Next, we will look briefly at how XML-based publication systems work, and what advantages they bring over electronic publication methods based on other digital formats.