The relationship between thermal conductivity and microstructures of aluminium nitride films is reported. Films were deposited on silicon substrates by magnetron sputtering of a pure Al target in nitrogen argon plasma at low temperatures (<300 °C) with thickness ranging from 150 to 3500 nm. Balanced and unbalanced magnetron configurations were used for different nitrogen contents in the gas phase. Various microstructures were thus created and their thermal conductivity was measured with the transient hot strip technique. Depending on the crystalline structure of the films, the bulk thermal conductivity of the AlN films at room temperature varied between 2 and 170 W m⁻¹ K⁻¹. Unbalanced magnetron allowed achieving highly dense (0 0 2) oriented AlN films with a grain size in the 100 nm range, a low oxygen content close to 0.5 at% and a resulting bulk thermal conductivity as high as 170 W m⁻¹ K⁻¹. Such a crystalline quality resulted from the ion energy involved in the growth process. In contrast, balanced magnetron led to weakly textured AlN films containing 5 at% oxygen with a grain size in the 30 nm range and a resulting thermal conductivity ranging from 2 to 100 W m⁻¹ K⁻¹ depending on the microstructure. Otherwise, the thermal boundary resistance between AlN films deposited by unbalanced magnetron and the silicon substrate was found to be as low as 1.0 × 10⁻⁸ K m² W⁻¹. Such a value was in good agreement with the thickness of the interfacial amorphous layer determined in the 2 nm range by high resolution transmission electron microscopy.