Introduction: AVH (Acute viral Hepatitis) is also a major health problem in younger children & adults in India. Causative agents of AVH, Hepatitis A (HAV) & Hepatitis E (HEV) viral infections are transmitted by faeco-oral route in developing countries. Several incidences of AVH have been reported in Rajasthan since 2011 Hence, the present study was aimed to study the incidence of HAV & HEV viral infections by Duplex Rt-PCR. Material & Method- Out of 9685 suspected Jaundice cases attending at MGMCH Jaipur. Total 300 HAV & HEV suspected cases who were having symptoms of jaundice less than 15 days of fever history were enrolled in this study. All these samples were collected from the patients attending Mahatma Gandhi Medical College & Hospital from periods of 2018-2020. These cases were tested for IgMAb for HAV & HEV and HAV & HEV infection by duplex RT-PCR. Result- Out of 300 viral hepatitis cases 119 cases were found HAV positive with incidence rate 1.22%. Among 300 cases ELISA, HAV IgM 35% (n=105) cases were found positive whereas HEV IgM 67% (n=29), HAV RTPCR 39.67% (n=119) whereas HEV RTPCR 14.67% (n=44) were found positive. Conclusion: The present study reveals the molecular identification and trends of the HAV & HEV viruses in the study area. The study also reveals about the early diagnosis of the HAV & HEV viruses in order to control the spread of these viruses efficiently. Keywords: AVH, HAV IgM, HEV IgM, HAV & HEV RTPCR.