Whole slide imaging (WSI) is a technique with both the scanning and viewing of digital images of the entire area of a glass pathology slide. The implementation of WSI has started to accelerate, and the usages of WSI are expected for variety of applications such as image analysis, education, conference, and remote diagnosis. However, for implementation of WSI to clinical applications, color variation in digital pathology images is one of the most important issues. The reasons for color variation of whole slide images are mainly in the two processes: staining tissue samples and scanning glass slides. This paper presents the methods and the results of the color correction of whole slide images, with consideration of these two reasons. For color variation caused by scanning devices, the characterization of the whole slide scanner was performed based on a traditional empirical model using a known color chart, where the color chart is a miniature transparent one arranged on a glass slide. In addition, it was also tested that color correction using Hematoxylin and Eosin stained mouse embryo slide instead of the color chart slide. For the color variation caused by staining conditions, the color distribution of images was corrected so as to fit to that of a reference image. Such correction is relatively easy for pathology image, because the color distribution of a stained pathology slide presents a characteristic color distribution decided by its staining method. The effectiveness of the color correction methods were confirmed for whole slide images of tissue samples stained by some typical staining methods.