Despite widespread aims to strengthen the Health Information System (HIS) as a tool for decentralised health care, there is a strong tendency in most developing countries that the HIS continues to reflect the central level's needs and requirements. The traditional design approach with little or no end user involvement results in a centralised HIS with an extensive, somewhat inappropriate, but also inflexible set of standards. Consequently, the HIS is not very useful for the wished-for decentralisation of health services, and there is an urgent need to redesign the existing HIS in order to make it locally relevant and appropriately decentralised. Based on a comparative case analysis of the HIS in Tanzania and Ethiopia, we offer practical recommendations on the way to achieve this redesign. A central design goal should be to achieve a balance between centralised control and local autonomy. Some degree of control over a decentralised HIS, including budgets and the use of resources, should be delegated to the district administration. In order to achieve the aim of a locally relevant, well-working HIS, it is necessary that appropriate authority, capacity and decentralised allocation of resources for HIS will be developed at the district and sub-district levels.