Dietary phenols are antioxidants, and their consumption might contribute to the prevention of cardiovascular disease. Coffee and tea are major dietary sources of phenols. Dietary phenols are metabolized extensively in the body. Lack of quantitative data on their metabolites hinders a proper evaluation of the potential biological effects of dietary phenols in vivo. The aim of this study was to identify and quantify the phenolic acid metabolites of chlorogenic acid (major phenol in coffee), quercetin-3-rutinoside (major flavonol in tea) and black tea phenols in humans, and determine the site of metabolism. Healthy humans (n = 20) with an intact colon participated in a dietary controlled crossover study, and we identified and quantified approximately 60 potential phenolic acid metabolites in urine. Half of the ingested chlorogenic acid and 43% of the tea phenols were metabolized to hippuric acid. Quercetin-3-rutinoside was metabolized mainly to phenylacetic acids, i.e., 3-hydroxyphenylacetic acid (36%), 3-methoxy-4-hydroxyphenylacetic acid (8%) and 3,4-dihydroxyphenylacetic acid (5%). In contrast, in seven humans without a colon, we found only traces of phenolic acid metabolites in urine after they had ingested chlorogenic acid and quercetin-3-rutinoside. This implies that the colonic microflora convert most of these dietary phenols into metabolites that then reach the circulation. Metabolites of dietary phenols have lower antioxidant activity than their parent compounds; therefore, the contribution of dietary phenols to antioxidant activity in vivo might be lower than expected from in vitro tests.