Fe/GaAs(001) is one of the leading candidate systems for achieving efficient spin-polarised injection. Although there have been numerous studies on the magnetotransport properties of Fe/GaAs(001) systems there is relatively little knowledge of the interface structure. In this study the atomic interface structure of Fe/GaAs(001) films has been investigated using both TEM and STEM techniques. The images show that as-deposited films consist of different interface structures. Although predominantly abrupt, the observation of partial mixing at the interface in some regions leads to a distribution of Schottky barrier heights. Ab-initio calculations were used to show that the partially mixed structure also forms interface resonance states. These states could provide a route for minority spin injection leading to bias dependent effects. Low temperature annealing has been shown to reduce the level of mixing in the films, thereby reducing the injection of minority spins through interface states. This explains the previously observed increase in injection efficiencies after annealing. Annealing also changes the shape of the Schottky barrier height distribution, explaining the increase in the effective Schottky barrier height after annealing. The magnetotransport properties of devices fabricated from the same film were investigated using both electrical and optical techniques. The magnetotransport properties show that reproducible devices can be created exhibiting well behaved characteristics, free from bias dependent phenomena. This is the first time that the atomic interface structure has been correlated to the magnetotransport properties in Fe/GaAs(001) films