In the field of biomaterials and biological compounds, ToF-SIMS has exhibited large interest due to high surface sensitivity, an information depth limited to the top-surface and molecular imaging capabilities. Selected examples given in this review concern recent applications like characterisation of engineered heterogeneous bioactive surfaces (including biosensors), combinatorial synthesis of peptides, molecular imaging of cells and quantification of biomolecules in real biological samples. These examples illustrate advantages and possible limitations of ToF-SIMS in this research field. Recent improvement with focus on these limitations is also briefly reviewed.