The International Civil Aviation Organization (ICAO) specifies that in the design phase of instrument flight procedures, an additional clearance may be added to an obstacle when flights are over mountainous terrain. This clearance increase can be up to 100 per cent of the minimum obstacle clearance (MOC). Airspace and instrument flight procedure designers usually face the problem of determining what value should be applied, since setting the maximum value of 100% often implies operational penalties, but there are no standardized criteria to determine lower values. The ICAO PANS-OPS indicates that the additional clearance over obstacles in mountainous areas is caused by two effects, both related to orography and wind speed. The first effect is due to the altimeter indication error. The second one is related to the loss of altitude when an aircraft is exposed to turbulence produced by mountain waves. This paper presents a methodology for determining the additional clearance to be applied over obstacles when, in the flight procedure design phase, the overflight of mountainous terrain is expected. Through this methodology, results have been achieved for the proposal of an appropriate additional clearance. The development of graphs and tables allows us to identify which additional value should be considered in each case.