Spatial genome organization in the cell nucleus plays a crucial role in the control of genome functions. Our knowledge about spatial genome organization relies on the advances in the genome imaging technologies and the biochemical approaches based on the spatially dependent ligation of the genomic regions. Fluorescent in situ hybridization using specific fluorescent DNA and RNA probes in cells and tissues with the spatially preserved nuclear and genome architecture (3D-FISH) provides a powerful tool for advancing our knowledge about genome structure and functions. Here, we describe the 3D-FISH protocols allowing such analysis in mammalian tissue in situ, including in the skin. These protocols include DNA probe amplification and labeling; tissue fixation; preservation and preparation for hybridization; hybridization of the DNA probes with genomic DNA in the tissue; and the post-hybridization tissue sample processing.