Resident macrophages in the rodent testis are heterogeneous in morphology, distribution and gene expression profiles. Recent studies have concentrated upon macrophages in the two main testicular compartments, the peritubular and interstitial macrophages. However, two other testicular compartments, specifically the rete testis (RT) and the subcapsular region (SC),have more direct contact with the external environment, and are implicated in initial responses to auto-immune challenges and ascending bacterial infections. Macrophage subsets were identified by immunofluorescence, using an antibody against F4/80 (all macrophages) in testis sections from adult mice expressing a GFP-transgene at the CX3CR1 (macrophage chemokine receptor) locus, Cx3cr1gfp/+.Macrophage subsets were further defined by expression of CD206 (anti-inflammatory) and MHCII (antigen-presentation) and quantified by stereology.Macrophage volume density was 9-fold higher in the peri-epithelium and interstitium of the RT than in the rest of the parenchyma. Whereas parenchymal peritubular macrophages were MHCII+CD206- and interstitial macrophages were MHCII-CD206+, most macrophages in the RT expressed both MHCII and CD206. Macrophages in the SC also expressed MHCII more frequently than macrophages in the parenchymal interstitium. A multiplex RNAseq analysis established that highly-purified macrophage preparations from mouse testes, comprising macrophages from all compartments, express genes encoding proteins involved in antigen-presentation (MHCII, Cd86, Ciita) and inhibition of inflammatory responses (Il10, Socs1, Nfkbiz, Stat6, Gata3, Inpp5d, Shpk).However, these cells displayed relatively low expression of genes involved in bacterial and viral responses, and were unresponsive to bacterial lipopolysaccharide. This study has identified a novel,large population of resident macrophages in the RT that is both antigen-presenting and anti-inflammatory,but deficient in anti-microbial responses. We hypothesize that these macrophages play the major role in inducing immune tolerance to spermatozoa emerging from the seminiferous tubules. Alterations to the protective function of these macrophages during inflammation and infection may lead to sperm autoimmunity or more severe inflammatory damage.