ABSTRACTThree-dimensional (3D) cell culture models such as spheroids and organoids are widely used in the field of experimental biology. To analyze these 3D experimental models, formalin-fixed paraffin-embedded (FFPE) sections are superior to whole-mount imaging for some experimental purposes, such as exploring samples with a depth limitation of primary antibody penetration immunohistochemically. However, tiny 3D cell culture samples are difficult to embed in paraffin and acquire appropriate sections. In this report, we optimized a protocol of paraffin embedding for spheroids and organoids. In addition, we compared FFPE sections with frozen sections in ratio of sample collection and section condition after staining, and could reproduce improved results reliably. The protocol we established could be widely used in many laboratories and become a useful technique for analyzing spheroids and organoids.