The adult mammary gland undergoes dynamic changes during puberty and the postnatal developmental cycle. The mammary epithelium is composed of a bilayer of outer basal, or myoepithelial, cells and inner luminal cells, the latter lineage giving rise to the milk-producing alveolar cells during pregnancy. These luminal alveolar cells undergo Stat3-mediated programmed cell death following the cessation of lactation. It is established that immune cells in the microenvironment of the gland have a role to play both in the ductal outgrowth during puberty and in the removal of dead cells and remodelling of the stroma during the process of postlactational regression. However, most studies have focussed on the role of the stromal immune cell compartment or have quantified immune cell populations in tissue extracts. Our recent development of protocols for deep imaging of the mammary gland in three dimensions (3D) has enabled the architectural relationship between immune cells and the epithelium to be examined in detail, and we have discovered a surprisingly dynamic relationship between the basal epithelium and leucocytes. Furthermore, we have observed morphological changes in the myoepithelial cells, as involution progresses, which were not revealed by previous work in 2D tissue sections and whole tissue. This dynamic architecture suggests a role for myoepithelial cells in the orderly progression of involution. We conclude that deep imaging of mammary gland and other tissues is essential for analysing complex interactions between cellular compartments.Abbreviations 2D, two dimensions; 3D, three dimensions; CD, cluster of differentiation; DAPI, 4 0 ,6-diamidino-2-phenylindole; DCIS, ductal carcinoma in situ; DCs, dendritic cells; DNA, deoxyribonucleic acid; GPI, glycosylphosphatidylinositol; H&E, haematoxylin and eosin; IgA, immunoglobulin A; K5, keratin 5; LIF, leukaemia inhibitory factor; MHCII, major histocompatibility complex class II; MIP, maximum intensity projection; MMPs, matrix metalloproteinases; NF-jB, nuclear factor kappa-light-chain-enhancer of activated B cells; SEMA, semaphorin; SMA, smooth muscle actin isoform a-actin; Stat, signal transducer and activator of transcription; TEBs, terminal end buds; Th, T helper; VEGF, vascular endothelial growth factor.