A slide storage, retrieval, transfer and scanning system for a slide scanner presents multiple components which work together in an automated fashion to streamline slide scanning in digital pathology. A slide storage assembly stores several slide baskets and can deliver a particular basket through a rotation mechanism. A slide basket transfer assembly retrieves the basket from the slide storage assembly and transfers the basket to a secondary location, where a slide transfer assembly retrieves a single slide from the basket and delivers the slide to a slide scanning stage for scanning.