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The Ugandan government continues to limit freedom of expression and association with human rights defenders being subjected to threats, intimidation and judicial harassment due to their legitimate human rights work. A number of human rights organisations have reported break-ins at their offices. Particularly at risk are human rights defenders advocating for the rights of lesbian, gay, bisexual, transgender and intersex (LGBTI) people.

In February 2014, President Museveni signed into law the 'Anti-homosexuality Bill' which criminalises what it terms “promotion of” and “aiding and abetting homosexuality” “or other related activities”, which are left undefined. While homosexuality was already criminalised under the country's penal code, the law goes further to impose harsh prison sentences to those convicted of advocating or supporting gay rights. In the face of these new developments, several LGBTI defenders have been forced to flee the country and many of their organisations have closed doors.

The government has clamped down on independent media and enacted legislation restricting civil and political rights and constraining the functioning of non-governmental organisations. On 14 March 2016, the 'Non-Governmental Organisations Act' (NGO Act) came into force, which includes some provisions containing vague wording which could be used to target legitimate human rights organisations. The NGO Act establishes a National Bureau of Non-Governmental Organisations which has the power to blacklist NGOs and restricts NGOs from engaging in activities that are "threatening national security" or “prejudicial to the security, interests or dignity of the people of Uganda”, leaving these terms undefined.