Motivated by constructions in topological data analysis and algebraic combinatorics, we study homotopy theory on the category of Čech closure spaces Cl, the category whose objects are sets endowed with a Čech closure operator and whose morphisms are the continuous maps between them. We introduce new classes of Čech closure structures on metric spaces, graphs, and simplicial complexes, and we show how each of these cases gives rise to an interesting homotopy theory. In particular, we show that there exists a natural family of Čech closure structures on metric spaces which produces a non-trivial homotopy theory for finite metric spaces, i.e. point clouds, the spaces of interest in topological data analysis. We then give a Čech closure structure to graphs and simplicial complexes which may be used to construct a new combinatorial (as opposed to topological) homotopy theory for each skeleton of those spaces. We further show that there is a Seifert-van Kampen theorem for closure spaces, a well-defined notion of persistent homotopy, and an associated interleaving distance. As an illustration of the difference with the topological setting, we calculate the fundamental group for the circle, ‘circular graphs’, and the wedge of circles endowed with different closure structures. Finally, we produce a continuous map from the topological circle to ‘circular graphs’ which, given the appropriate closure structures, induces an isomorphism on the fundamental groups.