Coffee, tea and caffeinated foods are popular in the world due to their high amount of caffeine, which are consumed daily by people in large quantities, and their effects on the body, especially the liver, are somewhat unknown, so this study was done with the aim of relationship between coffee and tea consumption and dietary intake of Caffeine on the serum liver enzymes and lipid profile. In this cross-sectional study the information of 8889 participants aged 35-70 years who referred to the Rafsanjan Cohort Study (RCS), a population-based prospective cohort that is a part of the Prospective epidemiological research studies in Iran (PERSIAN), was used. Demographic characteristics, medical history, consumption of coffee and tea, caffeine intake, and laboratory tests were collected. Dichotomous logistics regression models were used using crude and adjusted models to investigate the relationship between coffee, tea consumption, and caffeine intake with liver enzymes and lipid profile. Out of 8889 participants 4678 (52.6%) were female and 4211 (47.4%) were male. In older people, especially men, the consumption of tea and coffee increased and has a direct relationship with the abnormality of total cholesterol (TC) (OR 1.14; 95% CI 1.01 to 1.29). Also, it was observed that increased abnormal Alkaline phosphatase (ALP) (OR 1.22; 95% CI 1.01 to 1.52) and decreased abnormal serum glutamic-oxaloacetic transaminase (SGOT) (OR 0.65; 95% CI 0.46 to 0.93) were significantly associated with a high intake of caffeine. The other variables related to lipid profile and liver enzymes increased with increasing consumption of coffee, tea and intake of caffeine in participants, but did not show a significant increase. A high intake of caffeine and coffee and tea can have adverse effects on some liver enzymes and blood factors. Therefore, care should be taken when using these materials.