Organic materials are ubiquitous in all aspects of our daily lives. Increasingly there is a need to understand interactions between different organic phases, or between organic and inorganic materials (hybrid interfaces), in order to gain fundamental knowledge about the origin of their structural and functional properties. In order to understand the complex structure–property–processing relationships in (and between) these materials, we need tools that combine high chemical sensitivity with high spatial resolution to allow detailed interfacial characterisation. Analytical transmission electron microscopy (TEM) is a powerful and versatile technique that can fulfil both criteria. However, the application of analytical TEM to organic systems presents some unique challenges, such as low contrast between phases, and electron beam sensitivity. In this review recent analytical TEM approaches to the nanoscale characterisation of two systems will be discussed: the hybrid collagen/mineral interface in bone, and the all-organic donor/acceptor interface in OPV devices.