Resident and recruited olfactory epithelial macrophages participate in the regulation of the survival, degeneration, and replacement of olfactory sensory neurons (OSNs). We have reported that liposome-encapsulated clodronate (Lip-C) induced selective and statistically significant depletion of macrophages in the OE of sham and 48 h OBX mice (38 and 35%, respectively) that resulted in increased OSN apoptosis and decreased numbers of mature OSNs and proliferating basal cells compared to controls (Lip-O). The aim of this study was to identify molecular mechanisms by which the selective depletion of macrophages in the OE resulted in these cellular changes by using a microarray expression pattern analysis. A 2ϫ2 ANOVA identified 4,085 overall significantly (P Ͻ 0.01) regulated genes in the OE of Lip-O and Lip-C sham and 48 h OBX mice, and further statistical analysis using pairwise comparisons identified 4,024 genes that had either a significant (P Ͻ 0.01) treatment main effect (n ϭ 2,680), group main effect (n ϭ 778), or interaction effect (n ϭ 980). The mean hybridization signals of immune response genes, e.g., Cxcr4, and genes encoding growth factors and neurogenesis regulators, e.g., Hdgf and Neurod1, respectively, were primarily lower in Lip-C mice compared with Lip-O mice. Apoptosis genes, e.g., Bak1, were also differentially regulated in Lip-C and/or OBX mice. Expression patterns of selected genes were validated with real-time RT-PCR; immunohistochemistry was used to localize selected gene products. These results identified the differential regulation of several novel genes through which alternatively activated macrophages regulate OSN progenitor cell proliferation, differentiation, and maturation, and the survival of OSNs.clodronate; liposomes; microarray; immune response THE DYNAMIC ENVIRONMENT of the olfactory epithelium (OE), where olfactory sensory neurons (OSNs) undergo apoptosis and are replaced from a pool of basal progenitor cells throughout life (9,41,49), continues to provide insight into mechanisms of neuroprotection, neuronal apoptosis, and neurogenesis. More specifically, recent studies (6,23,33) on the interaction between the immune system and neurogenesis in the OE have strengthened the case for the participation of macrophages in the regulation of OSN survival and the proliferation, differentiation, and maturation of OSN basal progenitor cells in the unperturbed OE and during OE remodeling as a result of olfactory bulbectomy (OBX)-induced OSN apoptosis.