This paper describes the annual variations of the geometric heights of flight levels used for aircraft. The height difference between the isobaric surface corresponding to the flight level and the nominal flight level value is estimated from the measured geometric height of an aircraft by a height finding radar and the Mode C reported pressure altitude by the Secondary Surveillance Radar (SSR). The observed differences indicate a periodical variation of approximately twelve months. The seasonal trend of the difference between the geometric height H and the flight level FL, i.e., H-FL, is modelled by H-FL=C_1sin {C_2 (t-C_3)}+C_4+ε where t is the data acquisition time, ε is the residual and C_i (i=1, 2, 3, 4) are the model parameters. Several characteristics of H-FL are discussed herein.