We use a new data gathering method, “Web/URL citation,” Web/URL and Google Scholar to compare traditional and Web-based citation patterns across multiple disciplines (biology, chemistry, physics, computing, sociology, economics, psychology, and education) based upon a sample of 1,650 articles from 108 open access (OA) journals published in 2001. A Web/URL citation of an online journal article is a Web mention of its title, URL, or both. For each discipline, except psychology, we found significant correlations between Thomson Scientific (formerly Thomson ISI, here: ISI) citations and both Google Scholar and Google Web/URL citations. Google Scholar citations correlated more highly with ISI citations than did Google Web/URL citations, indicating that the Web/URL method measures a broader type of citation phenomenon. Google Scholar citations were more numerous than ISI citations in computer science and the four social science disciplines, suggesting that Google Scholar is more comprehensive for social sciences and perhaps also when conference articles are valued and published online. We also found large disciplinary differences in the percentage overlap between ISI and Google Scholar citation sources. Finally, although we found many significant trends, there were also numerous exceptions, suggesting that replacing traditional citation sources with the Web or Google Scholar for research impact calculations would be problematic.