We extend the scope of noncommutative geometry by generalizing the construction of the noncommutative algebra of a quotient space to situations in which one is no longer dealing with an equivalence relation. For these so-called tolerance relations, passing to the associated equivalence relation looses crucial information as is clear from the examples such as coarse graining in physics or the relation d(x, y) < ε on a metric space. Fortunately, thanks to the formalism of operator systems such an extension is possible and provides new invariants, such as the C * -envelope and the propagation number.After a thorough investigation of the structure of the (non-unital) operator systems associated to tolerance relations, we analyze the corresponding state spaces. In particular, we determine the pure state space associated to the operator system for the relation d(x, y) < ε on a path metric measure space.