Maize is the most important staple in sub-Saharan Africa (SSA), with highly seasonal production. High storage losses affect food security, but good estimations are lacking. A new method using focus group discussions (FGDs) was tested with 121 communities (1439 farmers, 52% women) in Kenya's six maize-growing zones, to estimate the maize losses to storage pests and analyze farmer practices. As control strategies, half of the farmers used chemical pesticides (49%), while hermetic bags (16%) and botanicals (15%) were also popular. Relative loss from weevils in the long rains was estimated at 23%, in the short rains 18%, and annually 21%. Fewer farmers were affected by the larger grain borer (LGB) than by maize weevils: 42% in the long rainy season and 32% in the short rainy season; losses from LGB were also smaller: 19% in the long season, 17% in the short season, and 18% over the year. Total storage loss, from both species combined, was estimated at 36%, or 671,000 tonnes per year. The greatest losses occur in the humid areas, especially the moist mid-altitudes (56%), and with smaller loss in the drylands (20–23%). Extrapolating the point data and overlaying with the maize production map shows the geographic distribution of the losses, with the most important area found around Lake Victoria. FGDs provide convenient and cheap tools to estimate storage losses in representative communities, but a total loss estimate of 36% is higher than is found in other studies, so its accuracy and framing effects need to be assessed. We conclude that storage pests remain a major problem, especially in western Kenya, and that the use of environmentally friendly technologies such as hermetic storage and botanicals needs more attention, both by the public extension service and private agrodealers.