Infectious diseases affect individuals (immunology) and populations (epidemiology). While these two scales of infection are intimately linked, the vast majority of studies of infectious diseases ignore or greatly simplify the effects of the other scale. As a result, public health programs can be ill-informed. Mathematical models that link the in-host and population scales of infection can better inform public health programs. However, these models can become very complex very quickly, even in their most simplified forms. We focus our mathematical modelling studies on the effects of immunity, the key outcome of infection at the in-host level (development of immune memory), and the key indicator of pathogen spread at the population level (through susceptibility and transmissibility). Immuno-epidemiological models that are well-informed by our in-host and population level studies are then developed. In this talk I will discuss our immunological, epidemiological, and immuno-epidemiolgical modelling studies of influenza, HIV, measles and pertussis. The effects of vaccination and waning immunity will be highlighted.