Abstract. We study spectral theory for bounded Borel subsets of R and in particular finite unions of intervals. For Hilbert space, we take L 2 of the union of the intervals. This yields a boundary value problem arising from the minimal operator D = 1 2πi d dx with domain consisting of C ∞ functions vanishing at the endpoints. We offer a detailed interplay between geometric configurations of unions of intervals and a spectral theory for the corresponding self-adjoint extensions of D and for the associated unitary groups of local translations. While motivated by scattering theory and quantum graphs, our present focus is on the Fuglede-spectral pair problem. Stated more generally, this problem asks for a determination of those bounded Borel sets Ω in R k such that L 2 (Ω) has an orthogonal basis of Fourier frequencies (spectrum), i.e., a total set of orthogonal complex exponentials restricted to Ω. In the general case, we characterize Borel sets Ω having this spectral property in terms of a unitary representation of (R, +) acting by local translations.The case of k = 1 is of special interest, hence the interval-configurations. We give a characterization of those geometric interval-configurations which allow Fourier spectra directly in terms of the self-adjoint extensions of the minimal operator D. This allows for a direct and explicit interplay between geometry and spectra.