Selenium is an important element in nutrition, showing great potential in the udder health of dairy goats and in the control of subclinical mastitis. However, there are few studies that evaluated the influence of selenium supplementation on subclinical mastitis in goats. The aim of this study was to evaluate the incidence of subclinical mastitis in dairy goats supplemented with organic selenium (Se yeast) in a semi-arid region. Sixteen Saanen × Toggenburg crossbred lactating goats were allocated randomly into two treatments: with and without addition of organic selenium (Se) to the concentrate. Milk samples were collected every 20days from each udder half to determine the somatic cell count (SSC), chloride content, pH, electrical conductivity, microbiological isolation, composition, and selenium contents. The highest serum selenium concentrations in the blood of these goats occurred at 42days of supplementation (P < 0.001). Goats which received organic selenium supplementation had higher serum selenium concentrations (P < 0.05). The milk composition variables did not differ (P > 0.05) between the tested treatments, teats, and collections. After 60days of supplementation, a difference was observed (P < 0.05) between treatments for SSC, chloride content, and pH. Addition of organic selenium to the diet of dairy goats after 60days of supplementation was promising in reducing the somatic cell count, consequently improving milk quality.