A digitization of the TEM pictures of fluorine-intercalated graphite fibers has been used to carry out quantitative measurements of the defect structure of this material. Emphasis is given to both the computer analysis technique and to the characterization of the defects. The amount of intercalation-induced disorder increases with increasing fluorine concentration. The fast Fourier transform of the digitized TEM image exhibits two diffuse spots, corresponding to the c-axis repeat distance of the intercalation compound. The length and width of the spots are a measure of the out-of-plane and in-plane disorder present in the fibers. From the fast Fourier transform, the distribution of interlayer repeat distances and the fraction of unintercalated graphite regions throughout the material is obtained. By selecting a small range of repeat distances and carrying out an inverse fast Fourier transform, the spatial distribution of material with a given repeat distance is determined. Regions with the same repeat distance are found to form islands. This particular feature of fluorine graphite intercalation compounds, as well as the nature of the microscopic defects and the staging behavior of fluorine-intercalated graphite fibers, are discussed in connection with the dual covalent and ionic nature of the carbon-fluorine bond in fluorine-intercalated graphite.