BackgroundChildhood mortality is high in sub-Saharan Africa. Mother-to-child transmission (MTCT) of HIV and congenital syphilis are among significant causes. Dual elimination of these two infections is one of the international goals. Community-based studies on the burden of HIV and syphilis among children will contribute to fine-tuning the interventions to achieve the elimination goal. This study aims to describe the prevalence of HIV and syphilis among children aged 0–36 months and associated factors in northern Tanzania.MethodsThis was a community-based cross-sectional study, which was conducted in all the seven districts of Kilimanjaro region. Multistage sampling was used, and a total of 2452 children aged 0 to 36 months and their primary caretakers were enrolled. Interviews were conducted with the mother/caretaker, and dried blood samples were collected from the children and processed for laboratory diagnosis of HIV and syphilis. HIV ELISA was first performed on all the samples. Positive samples of children < 18 months were confirmed using PCR.ResultsThe prevalence of HIV among 2452 children aged 0–36 months was 1.7% (n = 42). There was a significant difference in the distribution of HIV by age of the child, maternal antenatal attendance, and breastfeeding history.The prevalence of syphilis was 0.4% (n = 10). Five of the children were more than 1 year old. All children with a positive test for syphilis were from Moshi rural district, and their mothers consumed alcohol. No child was co-infected with HIV and syphilis.ConclusionsThough the prevalence of the two infections was low, detecting syphilis in children suggests a missed opportunity in screening women during pregnancy. The region may be on track with the goal to achieve dual elimination of mother-to-child transmitted HIV and syphilis. However, efforts are needed to reduce missed opportunities for screening women for syphilis and HIV early in pregnancy and retesting at 3rd trimester/delivery. Strategies to improve testing for HIV-exposed children are needed.