The aim of this study is to describe in what ways variation can be used in learning situations for pupils with autism to evoke deep understanding of activities in natural settings. The combination of variation and structure was designed to make each pupil discern new aspects of their learning objects. The analysis of the six participants' learning was based on the variation theory, and focused on how variation in the learning situation had affected the learning outcome. All six children who participated deepened their understanding of their learning objects, demonstrated by observable differences in performance of activities in which the targeted ability was included. The results are stable over time, showing the increased abilities in new situations during a six-month period. The study shows the importance of making the pupils focus on the connections between different aspects, rather than single aspects one at a time, to evoke deep understanding.