The influence of two types of structural defects on Schottky diodes in 4H-SiC is investigated. First, a structural transformation that takes place during oxidation or annealing of heavily n-doped wafers is studied using X-ray diffraction, high resolution TEM, secondary electron imaging (SEI), photoluminescence, and electrical measurements on Schottky diodes. Lamellae of 3C SiC with six bilayers are introduced primarily in the heavily doped substrates, and to a lesser extent in the lightly doped epilayers. Lowered Schottky barrier heights result and are spatially correlated to the 3C phase. The 3C lamellae exhibit charge contrast in SEI images where they intersect the surface. Second, we study isolated screw dislocations and show preliminary evidence that they are not the main factor controlling Schottky barrier height and ideality in Schottky diodes in lower-doped 4H-SiC wafers.