Analysis of the Fourier components of through-focal images in scanning transmission electron microscopy with a high angle annular dark field detector is used to assess illumination defocus values. The method is based on a least squares fitting of the peculiar dependence of Fourier components of the high angle annular dark field image on defocus. The validity of the method has been checked against simulations and experiments obtaining a good level of accuracy on the defocus measurement (δf=2 nm) for simulated specimen thickness up to 40 nm. The difference between simulated and experimental Fourier coefficients for large defoci can be used to estimate the specimen thickness at least up to 30 nm but with decreasing precision for larger thickness.