The number, size and distribution of the eyes are important quality parameters for hard and semi-hard cheeses. These quality factors are usually controlled by examination of the cheese after cutting or by taking out a small cylinder from the cheese. With such destructive approaches the time course changes in the product cannot be investigated which is a limiting factor in the improvement of knowledge on the mechanism involved in eye formation and growing. Therefore non-destructive techniques such as MRI and X-ray tomography allowing repeated measurements of individual products at consecutive times have been proposed. In this study, an MRI method for monitoring of eye growing in swiss-type cheese during ripening was evaluated and validated in order to exclude any effect of susceptibility artifacts on the eye volume estimation. Experiments were carried out on a 1.5 T scanner (Avanto, Siemens) using a 3D Turbo Spin Echo sequence. The impacts of echo train length and voxel size on the accuracy of eye volume estimation were investigated. An associated image processing method based on watershed segmentation for investigation of changes in eye characteristics, i.e. eye number, volume and spatial distribution during ripening was developed. Separating the overlapping eyes and eye labeling for individual monitoring were the important aspects of the image processing method. Finally, the MRI method was validated by comparison of the results of the cheese eyes volume measured by MRI with the volume estimation from the X-ray micro tomography experiments performed on the same cheese samples. The method was applied on industrial cheeses for studying the kinetic of the individual eyes growing in the product during the two-weeks hot room ripening.