The vertebrate photoreceptor cell contains an elaborate cilium that includes a stack of phototransductive membrane disks. The disk membranes are continually renewed, but how new disks are formed remains poorly understood. Here we used electron microscope tomography to obtain 3D visualization of the nascent disks of rod photoreceptors in three mammalian species, to gain insight into the process of disk morphogenesis. We observed that nascent disks are invariably continuous with the ciliary plasma membrane, although, owing to partial enclosure, they can appear to be internal in 2D profiles. Tomographic analyses of the basal-most region of the outer segment show changes in shape of the ciliary plasma membrane indicating an invagination, which is likely a first step in disk formation. The invagination flattens to create the proximal surface of an evaginating lamella, as well as membrane protrusions that extend between adjacent lamellae, thereby initiating a disk rim. Immediately distal to this initiation site, lamellae of increasing diameter are evident, indicating growth outward from the cilium. In agreement with a previous model, our data indicate that mature disks are formed once lamellae reach full diameter, and the growth of a rim encloses the space between adjacent surfaces of two lamellae. This study provides 3D data of nascent and mature rod photoreceptor disk membranes at unprecedented z-axis depth and resolution, and provides a basis for addressing fundamental questions, ranging from protein sorting in the photoreceptor cilium to photoreceptor electrophysiology.photoreceptor | cilium | EM tomography | disk morphogenesis P rimary cilia detect extracellular signals via membrane receptors or channels. The most elaborate of all cilia, the cilium that forms the vertebrate photoreceptor outer segment (OS), includes a large stack of membrane disks that extends distally from the transition zone, also known as the connecting cilium (1). The OS disks contain the visual receptor, opsin, and their tight packing allows for a high concentration of opsin within a confined space, thereby limiting the trade-off between visual sensitivity and spatial resolution. Turnover of OS disk membranes occurs throughout the lifetime of an animal (2) and requires the de novo synthesis and degradation of large amounts of OS proteins; on average, 9-10 billion opsin molecules are turned over every second in each human retina (3).A key event in OS disk turnover is the formation of disk membranes from newly synthesized molecules that are trafficked as vesicles from the endoplasmic reticulum (ER)/Golgi in the inner segment to the cilium (4, 5). Disk membrane morphogenesis is essential for the survival of photoreceptor cells. Orthologs of gene mutations that disrupt disk formation in mice have been linked to various retinal degenerations in humans; for example, in the rds mouse [mutant in peripherin-2 (Prph2)], disks do not develop from the end of the connecting cilium (6, 7), and in mice whose photoreceptors express mutant human prominin-1 (...