East Africa has been experiencing an increase in the occurrence of emerging infectious diseases such as yellow fever (YF) and dengue (DEN). Increasing frequency of YF activity in East Africa constitutes a re-emergence that was not detected for over 40 years. Additionally, DEN outbreaks have also increased in frequency and continue to be detected in Kenya and in neighboring countries like Tanzania, Somalia, Djibouti, Eritrea and South Sudan. The renewed vigor of YF and dengue fever (DF) re-emergence in East Africa presents a new challenge to public health in spite of the availability of a safe and effective vaccine for YF. However, there is need to understand the potential for YF and DEN transmission along the border areas of Kenya, because Kenya is classified among countries with medium to high risk for YF transmission. This classification was mainly based on historical data, proximity to countries reporting recent YF outbreaks, the presence of non-human primates known reservoirs for these viruses, unrestricted human movement and presence of potential vector mosquito species. Both YF and DEN share a similar niche in the ecosystem and are associated with Aedes mosquito species of the subgenus Stegomyia. While the factors leading to the re-emergence of these diseases are poorly understood, a better epidemiologic understanding relating to disease ecology including presence of potential vectors, their host blood feeding preferences, the vector competence in transmission of these viruses and evidence of virus circulation in human population, will guide assessment of disease risk in the target areas and help to prevent or mitigate severe outbreaks in this region.