Energy band alignment plays an important role in thin film solar cells. This article presents an overview of the energy band alignment in chalcogenide thin film solar cells with a particular focus on the commercially available material systems CdTe and Cu(In,Ga)Se2. Experimental results from two decades of photoelectron spectroscopy experiments are compared with density functional theory calculations taken from literature. It is found that the experimentally determined energy band alignment is in good agreement with theoretical predictions for many interfaces. These alignments, in particular the theoretically predicted alignments, can therefore be considered as the intrinsic or natural alignments for a given material combination. The good agreement between experiment and theory enables a detailed discussion of the interfacial composition of Cu(In,Ga)Se2/CdS interfaces in terms of the contribution of ordered vacancy compounds to the alignment of the energy bands. It is furthermore shown that the most important interfaces in chalcogenide thin film solar cells, those between Cu(In,Ga)Se2 and CdS and between CdS and CdTe are quite insensitive to the processing of the layers. There are plenty of examples where a significant deviation between experimentally-determined band alignment and theoretical predictions are evident. In such cases a variation of band alignment of sometimes more than 1 eV depending on interface preparation can be obtained. This variation can lead to a significant deterioration of device properties. It is suggested that these modifications are related to the presence of high defect concentrations in the materials forming the contact. The particular defect chemistry of chalcogenide semiconductors, which is related to the ionicity of the chemical bond in these materials and which can be beneficial for material and device properties, can therefore cause significant device limitations, as e.g. in the case of the CuInS2 thin film solar cells or for new chalcogenide absorber materials.