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Abstract Background Nigeria contributes significantly to the global burden of HIV, Hepatitis B and C infections, either singly or in combinations, despite progress in HIV care regionally and globally. Although some limited data on mono infection of HIV, Hepatitis B and C virus infections do exists, that of dual and triplex infections, including seroconversion and mother-to-child transmission (MTCT) rates necessary for planning to address the scourge of infections in pregnancy are not available. Objectives To determine the seroprevalence, rate of new infections, MTCT of dual and triple infections of HIV, Hepatitis B and C viruses and associated factors, among pregnant women in Nigeria. Method A multicenter prospective cohort study will be conducted in six tertiary health facilities randomly selected from the six geopolitical zones of Nigeria. All eligible pregnant women are to be tested at enrollment after informed consent for HIV, Hepatitis B and C virus infections. While those positive for at least two of the infections in any combination will be enrolled into the study and followed up to 6 weeks post-delivery, those negative for the three infections or positive for only one of the infections at enrolment will be retested at delivery using a rapid diagnostic test. On enrolment into the study relevant information, will be obtained, and laboratory test of CD4 count, liver function test and full blood counts, and prenatal ultrasonography will also be obtained/performed. Management of mother-newborns pairs will be according to appropriate national guidelines. All exposed newborns will be tested for HIV, HBV or HCV infection at birth and 6 weeks using PCR technique. The study data will be documented on the study case record forms. Data will be managed with SPSS for windows version 23. Ethical approval was obtained from National Health Research Ethics Committee (NHREC) (NHREC/01/01/2007–23/01/2020). Conclusion Pregnant women with multiple of HIV, HBV and HCV infections are at increased risk of hepatotoxicity, maternal and perinatal morbidity and mortality. Additionally, infected pregnant women transmit the virus to their unborn baby even when asymptomatic. Children born with any of the infection have significantly poorer quality of life and lower five-year survival rate. Unfortunately, the seroconversion and MTCT rates of dual or triplex infections among pregnant women in Nigeria have not been studied making planning for prevention and subsequent elimination of the viruses difficult. The study is expected to fill this knowledge gaps. Nigeria joining the rest of the world to eliminate the triple infection among children rest on the availability of adequate and reliable data generated from appropriately designed, and powered study using representative population sample. The establishment of the three-in-one study of prevalence, rate of new infection, rate and risk factor for MTCT of dual and triple infection of HIV, Hepatitis B and C viruses among pregnant women in Nigeria is urgently needed for policy development and planning for the improvement of the quality of life of mothers and the elimination of childhood triplex infection.