The introduction of Bt cotton in small-scale African farming systems raises the question of the technological efficacy of such cultivars in low-input rainfed agriculture conditions. Current surveys on Bt cotton in small-scale farming systems in South Africa suggest this transgenic crop is a key factor for increasing yields and farm income. This study was designed to assess the efficacy of the Bt cultivar under non-optimal conditions that prevail on small-scale farms. We thus carried out a 2-year comparative study on yield performances and boll distribution patterns of Bt and non-Bt cotton in 20 small-scale fields around Makhathini Flats (KwaZulu Natal, South Africa). A survey was also conducted on 86 farms to obtain yield results in a broader sample. In small-scale, low-input rainfed farming systems, productivity is extremely variable and the advantage of transgenic cotton over conventional varieties is not as easy to demonstrate as it is in large-scale, high-input irrigated farming systems. Given the high technological cost, adoption of transgenic crops may sometimes have a negative economic impact for farmers. Nevertheless, the use of transgenic varieties may be effective within the framework of an overall cropping intensification strategy, i.e. as an integrated pest management component and accompanied by fertilizer application and weed management recommendations.