The structure of mitochondrial creatine kinase is investigated by high-resolution shadowing at very low temperature and conventional negative staining. The electron microscopic images are analyzed with circular harmonic averaging, a method suited for the processing of single molecules. The rotational alignment and averaging is performed with the circular harmonic components, which allows data compression and several steps of noise reduction to be carried out within the averaging procedure. In addition, the symmetry can be deduced. For the mitochondrial creatine kinase, a fourfold symmetry is found that is compatible with the biochemical and biophysical characterization of the molecule.