The flu virus and antibiotic resistant bacteria are two good examples of how evolution affects your health. Without the ability to evolve, influenza would not jump species (remember bird flu and swine flu? they can infect humans because they evolve the ability to bind the proteins on human respiratory epithelia) and bacteria would not become resistant to the drugs we use to fight them.
At its most basic level, evolution is the acquisition of changes in the genetic material, which are then inherited by offspring. Bacteria have actually evolved a number of ways to evolve, via multiple types of reproductive methods.
How the immune system responds is also dictated by genetics - all proteins and enzymes in the body are encoded by your genes. What proteins your cells express (and thus what pathogens bind to and how the immune system cells interact) are the product of your genetics. There are even populations who are at low risk of HIV infection because they lack a protein on their immune cells!
So every day your health is affected by the genetics you were born with, as well as the genetics of the pathogens attacking your body - all products of biological changes from generation to generation, i.e. evolution.