AbstractPathological Anatomy is moving toward computerizing processes mainly due to the extensive digitization of histology slides that resulted in the availability of many Whole Slide Images (WSIs). Their use is essential, especially in cancer diagnosis and research, and raises the pressing need for increasingly influential information archiving and retrieval systems. Picture Archiving and Communication Systems (PACSs) represent an actual possibility to archive and organize this growing amount of data. The design and implementation of a robust and accurate methodology for querying them in the pathology domain using a novel approach are mandatory. In particular, the Content-Based Image Retrieval (CBIR) methodology can be involved in the PACSs using a query-by-example task. In this context, one of many crucial points of CBIR concerns the representation of images as feature vectors, and the accuracy of retrieval mainly depends on feature extraction. Thus, our study explored different representations of WSI patches by features extracted from pre-trained Convolution Neural Networks (CNNs). In order to perform a helpful comparison, we evaluated features extracted from different layers of state-of-the-art CNNs using different dimensionality reduction techniques. Furthermore, we provided a qualitative analysis of obtained results. The evaluation showed encouraging results for our proposed framework. Graphical Abstract