Cheese is a versatile nutrient-dense dairy product and it is of high importance to fully characterise its properties, e.g. texture and flavour, which contribute to the quality of this dairy food. These properties are substantially affected by the microstructure. This paper reviews recent developments in the study of microstructure of cheeses, using light microscopy (LM) and electron microscopy (EM) techniques, as well as the use of software to analyse microstructure images, i.e. micrographs, obtained. LM techniques used in the analyses of cheeses involve bright field, polarised, fluorescence and confocal scanning laser microscopy; whereas EM methods refer to scanning and transmission EM. Software used in microstructural image analyses is to quantify various components, such as protein and fat, and also to re-construct micrographs for further image processing. Finally, the use of microstructure techniques in the identification and localisation of bacterial cells within the cheese matrix is discussed. (C) 2013 Elsevier Ltd. All rights reserved.