a b s t r a c tIt is estimated that more than 95% of organic production is based on crop varieties that were bred for the conventional high-input sector. Recent studies have shown that such varieties lack important traits required under organic and low-input production conditions. This is primarily due to selection in conventional breeding programmes being carried out in the background of high inorganic fertilizer and crop protection inputs. Also, some of the traits (e.g., semi-dwarf genes) that were introduced to address problems like lodging in cereals in high-input systems were shown to have negative side-effects (reduced resistance to diseases such as Septoria, lower protein content and poorer nutrient-use efficiency) on the performance of varieties under organic and low-input agronomic conditions. This review paper, using wheat, tomato and broccoli as examples, describes (1) the main traits required under low-input conditions, (2) current breeding programmes for organic, low-input agriculture, (3) currently available breeding and/or selection approaches, and (4) the benefits and potential negative side-effects of different breeding methodologies and their relative acceptability under organic farming principles.