In an increasingly "publish or perish" clinical and academic environment, all clinicians and clinician-scientists involved in research must have a firm understanding of the measures commonly used to assess the quality of scientific journals and, by default, those extended to grade individual articles and authors. The publication of research is a vital part of clinical and experimental research, and citation analyses of research publications have increasingly been adopted as a means of assessing the apparent quality of journals and the research published therein. In the first of a series of articles for those embarking on ophthalmic and vision science research, this paper discusses the key features of citation analysis, concentrating on the 2004 Journal Citation Report figures for the field of ophthalmology that include 42 ophthalmology, vision science, physiological optics, and optometry journals. The Institute for Scientific Information (ISI) calculates a number of parameters including citation counts, Journal Impact Factor (JIF), Immediacy Index, and cited/citing half-life. This article discusses the methods of calculation and possible uses along with current controversies and potential abuses. The JIF and its relevance, potential bias, and limitations are discussed in depth as it has become the most widely used analysis of journal quality. The possible alternatives to ISI citation analysis are presented, and we conclude that citation analysis can be considered a reasonable measure of journal research quality only if used correctly.