Despite the strong linkage between environment and health, institutions responsible for these fields operate in largely fragmented ways with limited interaction. As illustrated in the recent engagement between health and urban planning institutions, inter-institutional cooperation could support more effective and politically acceptable solutions for both local and global problems. Analysis of three case-studies, from three different continents, shows that HIA might serve to promote synergies among health and environmental disciplines in different local contexts, and could lead to institutional and procedural changes that promote health. Case examples provided supportive evidence for these effects, despite differences in approaches to HIA and governance levels. Obstacles to the use of HIA for inter-institutional integration also differed between countries. Lessons learned could support cooperation in other common interests of health and environment disciplines such as research, training and preparedness, and mitigation of public health emergencies related to the environment.