A citation index is a bibliographic database that provides citation links between documents. The first modern citation index was suggested by information scientist Eugene Garfield in 1955 and created by him in 1964, and it represents an important innovation to knowledge organization and information retrieval. This article describes citation indexes in general, considering the modern citation indexes, including Web of Science, Scopus, Google Scholar, Microsoft Academic, Crossref, Dimensions and some special citation indexes and predecessors to the modern citation index like Shepard’s Citations. We present comparative studies of the major ones and survey theoretical problems related to the role of citation indexes as subject access points, recognizing the implications to knowledge organization and information retrieval. Finally, studies on citation behavior are presented and the influence of citation indexes on knowledge organization, information retrieval and the scientific information ecosystem is recognized.