In the Northern Ethiopian Highlands, ca.33% of the land is cropland, which is mainly cultivated by smallholders who based on indigenous knowledge plan their cropping system on the basis of spatio-temporal variability in rainfall. To understand the relationships between rainfall variability and cropping systems, a field campaign was undertaken in the rainy season of 2009 when 118 farmers were interviewed at different locations with different environmental characteristics. Five cropping systems were identified, each having a distinct cropping season length and crop association. Cropping systems with shorter cropping seasons were generally on the valleysides, whereas longer cycles occurred in the valley bottoms. The length of cropping season also increased from north-northeast to south-southwest. Crop associations within cropping systems also varied with altitude. Cropping systems changed in response to variation in annual rainfall. This resulted in shifts of cropping systems at catchment and regional scales, with cropping systems having longer cropping seasons where there was greater annual precipitation. The results were scaled up to the whole region by modelling the spatial distribution of cropping systems at a 8x8km(2) resolution over the period 1996-2009. The results indicate that indigenous knowledge is important when assessing the impact of climatic variability on agricultural production and that large inter-annual variability in the duration of crop cover in Northern Ethiopia might be an important, although generally overlooked, explanatory factor for explaining previous land degradation cycles.