Cu(In,Ga)Se$_2$ (CIGSe) absorber layers used in thin-film solar cells exhibit, when grown in a multistage process, compositional gradients of Ga and In. In this study, the correlations between the Ga gradient and the microstructure are studied by means of transmission electron microscopy (TEM) imaging combined with energy-dispersive X-ray spectroscopy (EDX), allowing the determination of structural defects and elemental distributions at identical sample positions. The occurrence of linear defects (dislocations) and planar defects (stacking faults and microtwins) of CIGSe layers was studied by means of TEM images. The Ga distributions obtained from EDX elemental distribution maps and structural parameters from the literature were used to calculate the lattice parameters c and a and the gradient dc/ dx perpendicular to the substrate. We found a correlation between the magnitude of dc/dx and the occurrence of dislocations within individual large grains. From the presented results, a threshold value of the Ga gradient of 12–13at.%/μm can be estimated for the formation of misfit dislocations.