Speckle patterns produced by multiple independent light sources are a manifestation of the coherence of the light field. Second-order correlations exhibited in phenomena such as photon bunching, termed the Hanbury Brown-Twiss effect, are a measure of quantum coherence. Here we observe for the first time atomic speckle produced by atoms transmitted through an optical waveguide, and link this to second-order correlations of the atomic arrival times. We show that multimode matter-wave guiding, which is directly analogous to multimode light guiding in optical fibres, produces a speckled transverse intensity pattern and atom bunching, whereas single-mode guiding of atoms that are output-coupled from a Bose-Einstein condensate yields a smooth intensity profile and a second-order correlation value of unity. Both first- and second-order coherence are important for applications requiring a fully coherent atomic source, such as squeezed-atom interferometry.