Two-dimensional almost-Riemannian structures are generalized Riemannian structures on surfaces for which a local orthonormal frame is given by a Lie bracket generating pair of vector fields that can become collinear. Generically, the singular set is an embedded one dimensional manifold and there are three type of points: Riemannian points where the two vector fields are linearly independent, Grushin points where the two vector fields are collinear but their Lie bracket is not and tangency points where the two vector fields and their Lie bracket are collinear and the missing direction is obtained with one more bracket. Generically tangency points are isolated. In this paper we study the Laplace-Beltrami operator on such a structure. In the case of a compact orientable surface without tangency points, we prove that the Laplace-Beltrami operator is essentially self-adjoint and has discrete spectrum. As a consequence a quantum particle in such a structure cannot cross the singular set and the heat cannot flow through the singularity. This is an interesting phenomenon since when approaching the singular set (i.e. where the vector fields become collinear), all Riemannian quantities explode, but geodesics are still well defined and can cross the singular set without singularities. This phenomenon appears also in sub-Riemannian structure which are not equiregular i.e. in which the grow vector depends on the point. We show this fact by analyzing the Martinet case.