This paper presents the results of a transient CFD analysis of the entire combustion system and the 1^st row of nozzle guide vanes of a small gas turbine combustor. The focus of the investigation is the fluid dynamics within the combustor casing and its impact on combustor internal flows. Full-scale compressible transient CFD computations of a single combustor can of a Siemens gas turbine were performed. The casing flow of a 1/6^th sector of the engine, corresponding to a single can was also simulated. Time dependent analyses of the combusting flow were performed for each case and the main features compared. In particular the main aerodynamic structures, such as vortex shedding and the Precessing Vortex Core (PVC), were characterised. A comparison was also made with non-combusting calculations to determine the effect of combustion. This work has taken the advantage of improvements in capabilities of numerical methods and computational power to develop design tools for gas turbine combustion systems. The work presented here is the first application of an improved turbulence model with the compressible solver in a gas turbine combustion system. This allows small scales of transient features to be captured. In addition, the presented work is the first simulation coupling the combustor aerodynamics to the casing flows.