Pakistan is seriously confronted by many complex and difficult environmental challenges related to air, water, soil, forests and food including issues such as climate change. The close link between environment and health is neither well understood nor appreciated. The annual cost of environmental degradation in Pakistan has been estimated to be around US$ 4.0 billion or at least 6% of the country’s GDP. Up to 35% of the burden of disease is attributable to environmental hazards and risk factors and most of this burden is preventable. A systematic process for identifying environmental health needs and issues as well as the efforts made by the government of Pakistan and the World Health Organization in establishing and launching an environmental health protection unit are described. Also presented are the mission, functions, structure (operational and logistical) and technical requirements as well as sustainability aspects of the environmental health protection unit.