Purpose Yerba mat, is widely consumed in South America as different beverages, such as mat, tea (roasted leaves) and chimarro (green dried leaves), and linked to health benefits, mainly attributed to chlorogenic acids (CGAs). Health effects of CGAs depend on their bioavailability, but such data are scarce. The aim of this study was to investigate the distribution of CGAs and metabolites in tissues, hepatic and plasmatic kinetic profile and urinary excretion after ingestion of mat, tea or 5-caffeoylquinic acid (5-CQA). Methods Wistar rats ingested mat, tea (MT) or 5-CQA (ST) and were killed after 1.5 h for tissue distribution analysis (pilot study) or at 0.5, 1, 2, 4 and 8 h for liver and plasma kinetics (main experiment). Urine was collected in metabolic cages. Biological samples were analyzed by UPLC-DAD-MS with and without incubation with beta-glucuronidase and sulfatase. Results CGAs and metabolites were detected in all tissues. Caffeic acid was the main compound in plasma up to 2 h after ingestion of mat, tea, while 5-CQA predominated in ST group. Concentration of microbial metabolites increased 4 h after gavage and reached higher amounts in MT plasma and liver, when compared to ST group. Approximately 4.0 % of compounds ingested by MT and 3.3 % by ST were recovered in urine up to 8 h after the gavage. Conclusion The study confirms that not only absorption, but also metabolization of CGAs begins in stomach. There were differences in compounds formed from mat, tea or isolated 5-CQA, showing that CGAs profile in food may influence qualitatively and quantitatively the metabolites formed in the body.