To reduce specic fuel consumption, it is expected that the next generation of aero-engines will operate with higher bypass-ratios, and therefore fan diameters, than current in-service architectures. These new propulsion systems will increase the nacelle size and incur in an additional overall weight and drag contribution to the aircraft. In addition, they will be installed more closely-coupled with the airframe, which may lead to an increase in adverse installation eects. As such, it is required to develop compact nacelles which will not counteract the benets obtained from the new engine cycles. A comprehensive investigation of the eects of nacelle design on the overall aircraft aerodynamic performance is required for a better understanding on the eects of aero-engine integration. This paper presents a method for the multi-objective optimisation of drooped and scarfed non-axisymmetric nacelle aero-engines. It uses intuitive Class Shape Tranformations (iCSTs) for the aero-engine geometry denition, multi-point aerodynamic simulation, a near-eld nacelle drag extraction method and the NSGA-II genetic algorithm. The process has been employed for the aerodynamic optimisation of a compact nacelle aero-engine as well as a conventional nacelle conguration. Subsequently, the designed architectures were installed on a conventional commercial transport aircraft and evaluated at dierent installation positions. A novel thrust-drag bookkeeping method has been used to 1