We study the regularity of the solutions of second order boundary value problems on manifolds with boundary and bounded geometry. We first show that the regularity property of a given boundary value problem (P, C) is equivalent to the uniform regularity of the natural family (Px, Cx) of associated boundary value problems in local coordinates. We verify that this property is satisfied for the Dirichlet boundary conditions and strongly elliptic operators via a compactness argument. We then introduce a uniform Shapiro-Lopatinski regularity condition, which is a modification of the classical one, and we prove that it characterizes the boundary value problems that satisfy the usual regularity property. We also show that the natural Robin boundary conditions always satisfy the uniform Shapiro-Lopatinski regularity condition, provided that our operator satisfies the strong Legendre condition. This is achieved by proving that "well-posedness implies regularity" via a modification of the classical "Nirenberg trick". When combining our regularity results with the Poincaré inequality of (Ammann-Große-Nistor, preprint 2015), one obtains the usual well-posedness results for the classical boundary value problems in the usual scale of Sobolev spaces, thus extending these important, wellknown theorems from smooth, bounded domains, to manifolds with boundary and bounded geometry. As we show in several examples, these results do not hold true anymore if one drops the bounded geometry assumption. We also introduce a uniform Agmon condition and show that it is equivalent to the coerciveness. Consequently, we prove a well-posedness result for parabolic equations whose elliptic generator satisfies the uniform Agmon condition. 12 4. Variational boundary conditions and regularity 13 4.