Let L be an elliptic differential operator with bounded measurable coefficients, acting in Bochner spaces L p (R n ; X) of X -valued functions on R n . We characterize Kato's square root estimates √ Lu p ∇u p and the H ∞ -functional calculus of L in terms of R-boundedness properties of the resolvent of L, when X is a Banach function lattice with the UMD property, or a noncommutative L p space. To do so, we develop various vector-valued analogues of classical objects in Harmonic Analysis, including a maximal function for Bochner spaces. In the special case X = C, we get a new approach to the L p theory of square roots of elliptic operators, as well as an L p version of Carleson's inequality.