The organisational hierarchy defines the organisation structure of the DHIS2 instance, such as how the health facilities, administrative areas and other geographical areas are arranged with respect to each other. It is essentially the "where" dimension of DHIS2, similar to how periods represent the "when" or time dimension. DHIS2 is structured so that the organisational unit hierarchy is a geographical hierarchy, and the GIS module depends on this. Non-geographical hierarchies are discouraged, and would better to be represented through the use of organisational unit groups. This dimension to the data is defined as a hierarchy with one root unit (e.g. Ministry of Health or a country) and any number of levels and nodes below. Each node in this hierarchy is called an organisational unit in DHIS2.

The design of this hierarchy will determine the geographical units of analysis available to the users as data is collected and aggregated in this structure. There can only be one organisational hierarchy at the same time so its structure needs careful consideration.

Additional hierarchies (e.g. parallel administrative boundaries to the health care sector) can be modeled using organisational groups and group sets, but the organisational hierarchy is the main vehicle for data aggregation on the geographical dimension. Typically national organisational hierarchies in public health have 4-6 levels, but any number of levels is supported.

The hierarchy is built up of parent-child relations. For instance a country might have eight provinces, and each province again might have a number of districts as their children. Normally the health facilities (from which data is typically collected) will be located at the lowest level, but they can also be located at higher levels, e.g. national or provincial hospitals, so skewed organisational trees are supported (e.g. a leaf node can be positioned at level 2 while most other leaf nodes are at level 5).

Note that it is quite easy to make changes to the upper levels of the hierarchy at a later stage, the only problem is changing organisational units that collect data (the leaf nodes), e.g. splitting or merging health facilities. Aggregation up the hierarchy is done based on the current hierarchy at any time and will always reflect the most recent changes to the organisational structure.