Epidemiological and medical anthropological investigations suggest that flavanol‐rich foods exert cardiovascular health benefits. Chocolate is a food that is known to be rich in flavonoids, the main flavonoids in chocolate is flavan‐3‐ol epicatechin. However, the bioavailability and the biological effects of the chocolate flavonoids are poorly understood. The objective was to quantify the effect of epicatechin ingested via dark chocolate on changes in biochemical parameters. Also to determine if the ingestion of dark chocolate rich in epicatechin exert anti‐gentoxic effect in buccal epithelial cells of young adults. Thirty apparently healthy men (20 to 30 years old) participated in a randomized, double‐blind, placebo‐controlled crossover trial during tree months. Consumption of dark chocolate or low‐flavanol chocolate (2 g) was daily ingested. Genotoxicity in buccal epithelial cells was determined by identify and quantify micronuclei in the exfoliated cells of oral mucosa in individuals before the intervention with chocolate, during the intervention (every mounth) and after the intervention. The concentration of glucose, cholesterol, HDL and LDL in plasma was determined before and after the ingestion of dark chocolate or low‐flavanol chocolate. The presence and amount of genotoxic damage was correlated with the main genotoxic factors (alcohol intake, smoking and obesity) and the ingestion of dark chocolate or low‐flavanol chocolate.Support or Funding InformationThis research was supported by the Research Chair Funds for Full Time Professors (2014) of Autonomous University of Baja California (UABC), program Number 3888. The authors would like to acknowledge Consejo Nacional de Ciencia y Tecnología (CONACYT) in Mexico.