Let R be a root system (in the sense of Bourbaki) in a finite dimensional real inner product space V. A subset P ⊂ R is closed if α, β ∊ P and α + β ∊ R imply that α + β ∊ P. In this paper we shall classify, up to conjugacy by the Weyl group W of R, all closed sets P ⊂ R such that R\P is also closed. We also show that if θ:R —> R′ is a bijection between two root systems such that both θ and θ-1 preserve closed sets, and if R has at most one irreducible component of type A1, then θ is an isomorphism of root systems.