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The National Library of Uganda has four major departments namely:

Office of the Director
The office of the Director is responsible for Board matters, policy formulation and execution, finance, overall administration, staff matters and liaison with other government agencies. The department is headed by the Director who is assisted by the Deputy Director, Senior Accountant, Office Superintendent and support staff.

Technical Service Department
TSD is responsible for acquiring and processing information materials for the National Library of Uganda through purchase, donations or exchange and legal deposits.  It also coordinates book donations for public and community libraries throughout Uganda.  Donations are also extended to other libraries in the country. TSD compiles and publishes the National Bibliography of Uganda, maintains the National Library website and creates and manages National Library databases.

Inspection, Research, and Extension Services Department
Inspection Research and Extension Services department is responsible for promoting the reading culture through libraries and other reading activities, monitoring of library services, developing guidelines and standards for public and community libraries and publishing for the National Library of Uganda.

Information and Referral Service Department
The Information Referral Services Department is responsible for maintaining and preserving the National library collection and providing reference and research materials and services to users.

Library stock
The stock of the library is in five different sets of collections.
- The National Collection
- The African Collection
- The reference Collection
- The Special Collection
- Newspapers and Serial Publications