We have recently reported that macrophages are generated in dental pulp-like tissues engineered by culturing stem cells from human exfoliated deciduous teeth (SHED) in a scaffold placed in the canal space of human tooth slice. We hypothesized that these macrophages are activated to M1 and/or M2 directions, and participate in absorbing the scaffold by their phagocytic ability. Thus, to examine the types of activated macrophages in the engineered dental pulp-like tissue, we performed immune-laser capture microdissection (LCM) of CD68 (anti-human macrophages)-immunoreactive cells. The CD68-immunoreactive cells in the pulp-like tissues that had been fixed with formaldehyde, demineralized with 10% formic acid, and embedded in paraffin were retrieved by LCM and analyzed for the mRNA expression of M1 and M2 macrophage markers with real-time PCR. Results demonstrated that the expression level of CCL18, an M2 macrophage marker, was significantly higher in CD68-immunoreactive cells retrieved from the area where most of the scaffold was absorbed, as compared with CD68-immunoreactive cells in the scaffold-remaining area. On the other hand, the mRNA expression level of inducible nitric oxide synthase (iNOS), an M1 macrophage marker, was significantly decreased in the scaffold-remaining area. These results suggested that macrophages activated to the M2 direction are preferentially distributed in the scaffold absorption area of the engineered dental pulp-like tissues. The immune-LCM method presented here allows for the quantitative analysis of gene expression in paraffin-embedded tissue sections from specimens that have been demineralized. This immune-LCM method constitutes a new approach for histochemistry of mineralized tissues such as bone and teeth, opens the door for the acquisition of new data from archived specimens, and is suited for the analysis of relatively rare cell types within a tissue.