While the geometry of aerospace assemblies is carefully controlled, for many industrial applications such as marine structures bond line thickness can vary significantly. In this study epoxy adhesive joints of different thicknesses between aluminium substrates have been characterized using physico-chemical analyses (differential scanning calorimetry, DSC; dynamic mechanical analysis, DMA; spectroscopy), nano-indentation and mechanical testing. Thermal analyses indicated no influence of thickness on structure. Nano-indentation revealed no evidence of an interphase at the metal/epoxy interface, nor any change in modulus for different thicknesses, though Raman spectroscopy suggested there may be slight variations in composition close to the substrates. However, mechanical testing using the modified Arcan fixture indicated a significant drop in strength and failure strain under pure tension and a smaller reduction for tension/shear and pure shear loads as thickness increased. Examination of sections through joints did not indicate any physical reason for this, but numerical analysis of the stress state revealed larger stress concentration factors for tensile loading in thick joints, which may explain the thickness effect. It is recommended that joint thickness should be kept below 0.8 mm to avoid obtaining artificially low values with the Arcan test.