Introduction The epidemiology of hepatitis, which is apparently endemic in Asia, is still poorly documented in Malaysia. Available statistics are modelled estimates based on expert input or estimated from small studies on special populations. We therefore determined the prevalence of chronic hepatitis B and C in Malaysia based on a large sample data from a screening campaign. Methods A total of 10,914 subjects participated in the hepatitis screening campaign in 2018 and 2019. A low-cost Point-of-care test, which has previously been validated, was used to screen for HBsAg and anti-HCV. All screen positive subjects were recalled to undergo confirmatory serology tests and nucleic acid tests. Results We estimated 1.17% or 238,971 Malaysian adults aged 20 or older had chronic HBV, while only 0.74% or 151,144 adults had chronic HCV. Young adults below age 30 years had very low prevalence of HBV (0.09%). Women had lower prevalence of HBV and HCV, Chinese had the highest prevalence of HBV while Malay had the highest prevalence of HCV. Conclusion Young adults seems to be protected from HBV perhaps owing to the introduction of universal HBV vaccination since 1989. Chronic HBV however remains prevalent in older adults especially among the Chinese. Chronic HCV is uncommon in Malaysia.