The process by which a micro-organism causes disease is known as pathogenesis. Despite extensive research into AIDS pathogenesis since 1981, large gaps remain in our knowledge of the steps between HIV infection and the development of AIDS. A simple concept of pathogenesis is with one factor causing a change in another, which in turn changes another, and so on. For example, A affects B, B affects C, and so on, until Y affects Z.

A simple orthodox view of pathogenesis for AIDS is that HIV infection leads to loss of CD4 T-cells and this loss of T-cells results in increased susceptibility to AIDS-related conditions.

In reality there are many more steps in the pathogenesis of AIDS. There are also human and environmental factors influencing almost every step, and changes in one factor may influence other functions of the body along other pathways.