Aerodynamic drag and bearing friction are the main sources of standby losses in the flywheel rotor part of a flywheel energy storage system (FESS). Although these losses are typically small in a well-designed system, the energy losses can become significant due to the continuous operation of the flywheel over time. For aerodynamic drag, commonly known as windage, there is scarcity of information available for loss estimation since most of the publications do not cover the partial vacuum conditions as required in the design of low loss energy storage flywheels. These conditions cause the flow regime to fall between continuum and molecular flow. Bearings may be of mechanical or magnetic type and in this paper the former is considered, typically hybridized with a passive magnetic thrust bearing. Mechanical bearing loss calculations have been extensively addressed in the open literature, including technical information from manufacturers but this has not previously been presented clearly and simply with reference to this application. The purpose of this paper is therefore to provide a loss assessment methodology for flywheel windage losses and bearing friction losses using the latest available information. An assessment of windage losses based on various flow regimes is presented with two different methods for calculation of windage losses in FESS under rarefied vacuum conditions discussed and compared. The findings of the research show that both methods closely correlate with each other for vacuum conditions typically required for flywheels. The effect of the air gap between the flywheel rotor and containment is also considered and justified for both calculation methods. Estimation of the bearing losses and considerations for selection of a low maintenance, soft mounted, bearing system is also discussed and analysed for a flywheel of realistic dimensions. The effect of the number of charging cycles on the relative importance of flywheel standby losses has also been investigated and the system total losses and efficiency have been calculated accordingly.