A method of calibration of a navigation and pointing system comprising a navigation unit integrally connected to a pointing device, the navigation unit being configured to measure the position and the orientation of a reference system of said navigation unit, the pointing device comprising means for emitting a beam in a pointing direction and means for varying the pointing direction, the pointing device being configured to measure a pointing signal, as a function of the pointing direction in a reference system linked to the pointing device, the calibration method comprising the following steps of calibration of the angles between the reference system of said navigation unit and the reference system linked to the pointing device: a. Estimating an approached navigation reference system, the approached navigation reference system being inclined with respect to the navigation reference system with misalignment Euler angles (Φ, θ, Ψ); b. Selecting a first planar surface; c. Determining a vector (N 8) normal to said first planar surface in the navigation reference system; d. Directing the navigation and pointing system in a plurality of distinct angular orientations with respect to the first planar surface, said plurality of angular orientations being determined in the reference system of the navigation unit; e. Varying the pointing direction so as to acquire, by means of the pointing device, for each of the orientations of said plurality of orientations with respect to the first planar surface, a series of pointing measurements along a scan line (41, 42, 43) on the first planar surface; f. Processing each of said series of pointing measurements along a scan line (41, 42, 43) on the first planar surface, so as to determine, in the reference system linked to the pointing device, an approached direction vector ( û 1, û 2, û 3) of each scan lines (41, 42, 43) on the first planar surface; g. Processing a plurality of approached direction vectors ( û 1, û 2, û 3)of a plurality of scan lines (41, 42, 43) on the first planar surface, to deduce therefrom an approached normal vector (N̂ 8) of the first planar surface; h. Calculating at least one misalignment angle (Φ, θ, Ψ) between the approached normal vector (N̂ 3) determined at the previous step in the approached navigation reference system and the normal vector (N 8) determined a step c) in the reference system of the navigation unit. a. Estimating an approached navigation reference system, the approached navigation reference system being inclined with respect to the navigation reference system with misalignment Euler angles (Φ, θ, Ψ); b. Selecting a first planar surface; c. Determining a vector (N 8) normal to said first planar surface in the navigation reference system; d. Directing the navigation and pointing system in a plurality of distinct angular orientations with respect to the first planar surface, said plurality of angular orientations being determined in the reference system of the navigation unit; e. Varying the pointing direction so as to acquire, by means of the pointing device, for each of the orientations of said plurality of orientations with respect to the first planar surface, a series of pointing measurements along a scan line (41, 42, 43) on the first planar surface; f. Processing each of said series of pointing measurements along a scan line (41, 42, 43) on the first planar surface, so as to determine, in the reference system linked to the pointing device, an approached direction vector ( û 1, û 2, û 3) of each scan lines (41, 42, 43) on the first planar surface; g. Processing a plurality of approached direction vectors ( û 1, û 2, û 3)of a plurality of scan lines (41, 42, 43) on the first planar surface, to deduce therefrom an approached normal vector (N̂ 8) of the first planar surface; h. Calculating at least one misalignment angle (Φ, θ, Ψ) between the approached normal vector (N̂ 3) determined at the previous step in the approached navigation reference system and the normal vector (N 8) determined a step c) in the reference system of the navigation unit.