Citation analysis has evolved over the last 50 years as one parameter for assessing the quality of research published in scientific, technology and social science journals. This is based on the assumption that influential research is widely cited by other scientists and clinicians. With the advent of the Internet, Journal Citation Reports from the Institute for Scientific Information (ISI-JCR) have become widely available to individuals and institutions. In an increasingly competitive research environment, aspects of citation analysis have been suggested as simple proxy, objective measures to evaluate the research quality of a journal, published articles, research institutions and even individual researchers. This review article provides an overview of citation analysis, including definitions, uses of these reports, and related controversies and potential abuses. As it has become the most commonly used indicator, there is a particular focus on the use of the Journal Impact Factor (JIF). This is a widely quoted measure indicating the frequency with which the average article published in a journal of interest will be quoted within a specified time frame that therefore allows approximate comparisons of journals within a particular field of interest. Given the relative paucity of information in this area, emphasis is placed on citation analysis within ophthalmology, in particular in regard to the 43 ophthalmology, vision science and optometry journals that are listed in the ISI-JCR 2001 reports.