Climate variability directly affects traditional low input and rain-fed farming systems, but few studies have paid attention retrospectively to the cropping system's ability to mitigate climate risk. This study analyzes the impacts of rainfall variability on farmers' seed variety losses over time, considering changes in smallholder farming systems. The cropping system dynamics, in favoring maize at the expense of sorghum and pearl millet, have induced an increasing risk of seed loss during drought. Combining ecological anthropology and climatology, a retrospective survey asking farmers about the period 1961-2006 was carried out at three altitudinal levels (750, 950, and 1100 m) on the eastern slope of Mount Kenya. Over that period, based on 3204 seed loss events reported orally and independently by 208 farmers, the probability to lose sorghum seed (0.056-0.065) was significantly lower than the probability to lose maize seed (0.071-0.087). All crops were more impacted by droughts than by very wet years. Seed loss probability increased for rainy seasons shorter than 50 days, with less than 28 rain days, and with a precipitation amount under 400 mm. Losses are almost linearly related to the frequency of rain days. Logistic regression confirmed that a change in cropping systems, favoring maize at the expense of sorghum and pearl millet, increased the risk of seed losses due to drought over the 46-yr period.