The structure of foods is a complex amalgam of different biomolecules that are structurally diverse and that exhibit heterogeneity within their own biomolecule type. The interactions among these components control the structure and texture of foods, in addition to indirectly influencing other properties such as colour, flavour, and aroma. Molecular modelling has been used increasingly over the past few decades to help understand the interactions that control food structure and, as modelling techniques and hardware improve, will become an ever more important tool for food scientists. In this chapter, we will review aspects of food structure formation that are highly amenable to the modelling approach. The review will concentrate on the modelling of biomolecule self-association and gel formation and how this contributes to food structure and texture. Modelling the development of gelling agents into 3D fibrillar structures is a very important and challenging task and can provide significant insights to food chemists and biologists. This chapter gives an overview of recent studies focusing on how modelling and computer simulations can be used to investigate the relationship between the microscopic and macroscopic properties of different building blocks, such as oleogelators, polysaccharides, or proteins, that are commonly used for formulating food products.