According to Science Watch, the 10 most cited journals based on 1999-2009 totals are: "Journal of Biological Chemistry" (1.65 million), "Proceedings of the National Academy of Science" (1.4 million), "Nature" (1.2 million), "Science" (1.1 million), "Physical Review Letters" (884,911), "Journal of the American Chemical Society" (881,457), "Physical Review B" (612,337), "Astrophysical Journal" (581,299), "New England Journal of Medicine" (568,698) and "Applied Physics Letters" (549,224). Science Watch uses the Thomson-Reuters citation index.
Based on 20010-2012 data, SCImago Journal and Country Rank’s top 10 are: "Proceedings of the National Academy of Science" (119,356), "Nature" (104,068), "PLoS One" (103,109), "Journal of the American Chemical Society" (102,432), "Science" (88,919), "New England Journal of Medicine" (65,891), "Physical Review Letters" (65,309), "Journal of Biological Chemistry" (62,587), "Angewandte Chemie -- International Edition" (59,703) and "Physical Review B -- Condensed Matter and Materials Physics" (58,343). SCImago uses the Scopus citation index.