Three phenotypes for urolithin production after ellagitannin and ellagic acid intake are consistently observed in different human intervention trials. Subjects can be stratified into three urolithin-producing groups. “Phenotype A” produced only urolithin A conjugates, which included between 25 and 80% of the volunteers in the different trials. “Phenotype B” produced isourolithin A and/or urolithin B in addition to urolithin A, this being the second relevant group (10–50%). “Phenotype 0” (5–25%) was that in which these urolithins were not detected. The three phenotypes were observed independently of the volunteers’ health status and demographic characteristics (age, gender, body mass index (BMI)) and of the amount or type of ellagitannin food source ingested (walnuts and other nuts, strawberries, raspberries, and other berries or pomegranates). Interestingly, a higher percentage of phenotype B was observed in those volunteers with chronic illness (metabolic syndrome or colorectal cancer) associated with gut microbial imbalance (dysbiosis). These urolithin phenotypes could show differences in the human gut microbiota and should be considered in intervention trials dealing with health benefits of ellagitannins or ellagic acid. Whether this phenotypic variation could be a biomarker related to differential health benefits or illness predisposition deserves further research.