Gaseous Bose-Einstein condensates of 2-3 x 10(6) 23Na atoms were loaded into a microfabricated magnetic trap using optical tweezers. Subsequently, the condensates were released into a magnetic waveguide and propagated 12 mm. Single-mode propagation was observed along homogeneous segments of the waveguide. Inhomogeneities in the guiding potential arose from geometric deformations of the microfabricated wires and caused strong transverse excitations. Such deformations may restrict the waveguide physics that can be explored with propagating condensates. Finer perturbations to the guiding potential fragmented the condensate when it was brought closer to the surface.