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A cross-sectional study was conducted to investigate the risk factors for sub-clinical mastitis (SCM) in Mbarara District, an intensive dairy production region of Uganda where hand-milking is dominant. In 30 farms, herd-level milking practices and SCM prevalence were studied. The SCM prevalences were 68.6% (417/608, 95% confidence interval (CI) 64.9-72.2%) and 39.2% (946/2,411, 37.3-41.2%) at the cow- and quarter-levels, respectively. A preventive factor for SCM was cow calmness at the end of milking (OR 0.20, 95%CI 0.05-0.79, P=0.021)