· High enrolments against limited facilities.
· Low transition rates across the system
· Inadequate and poorly trained teachers.
· Gender imbalances.
· HIV/AIDS, which has caused death of pupils, teachers and parents with trauma and stigma associated with HIV/AIDS also affecting learning programmes.
· Armed conflict/insurgency, especially in North/East Uganda, which has caused instability and displaced families, hence hampering education programmes
· Prohibitive cultural practices and attitudes, mostly affecting girls.
· Geographical barriers