Cheese is a classical dairy product, which is strongly judged by its appearance and texture; hence, a renewed interest in its microstructure has been on the rise, as sophisticated techniques of analysis become more and more informative and widely available. Processing parameters that affect microstructure play a dominant role upon the features exhibited by the final product as perceived by the consumer; rational relationships between microstructure (which includes biochemical and microbiological indicators), and quality and safety of the products are accordingly required. Subsequent to that extra fundamental knowledge, technological innovations may eventually improve current cheesemaking processes, and permit mechanistic design of novel ones. This review thus focuses on recent advances pertaining to the microstructure of cheese, and discusses them in a logical and critical manner.