Over 1.4 million people are living with HIV in Uganda, with 67% of adults on antiretroviral treatment (ART) and only 47% of children. Young people – especially girls – are particularly vulnerable to HIV. Men who have sex with men (MSM) are also especially vulnerable. In 2014, the passing of the anti-homosexuality law created a hostile environment for the lesbian, gay, bisexual and transgender (LGBT) community, making access to health information and services extremely difficult and dangerous.

In 2017, CHAU reached over 6,000 people with HIV prevention services and almost 4,000 people with integrated HIV/SRHR services. CHAU currently works with the Alliance on a range of programmes that aim to tackle HIV in Uganda using a multi-pronged approach. The SIDA SRHR Umbrella Programme builds on the institutional and technical capacity of civil society organisations (CSOs) and will provide funding at a national and district level for 5 years.

CHAU also partners with the Alliance Secretariat on PITCH, a programme that focuses on advocacy as a way to empower key populations and strengthen the capacities of local CSOs to respond to HIV in Uganda. EJAF Uganda is a programme supported by the Elton John AIDS Foundation which aims to increase access to and uptake of STI & HIV services for LGBT people, particularly HIV counselling and testing (HCT), combination prevention, and ART. CHAU also implemented the SHARP project in the past, which supported the sexual health and rights of MSM.

CHAU's work with young people has also continued through READY Teens, a project that focuses on 10-19 year olds living with and most affected by HIV. This builds on the previous work with the Link Up project, an ambitious, five-country programme which aimed to improve the sexual and reproductive health and rights (SRHR) of more than one million young people.

Historically, the Alliance operated a country office in Uganda until 2013, when it was transitioned to an independent and autonomous organisation known as Community Health Alliance Uganda (CHAU).