We report the successful imaging of flux vortices in single crystal MgB2 using transmission electron microscopy. The specimen was thinned to electron transparency (350 nm thickness) by focussed ion beam milling. An artefact of the thinning process was the production of longitudinal thickness undulations of height 1-2 nm in the sample which acted as pinning sites due to the energy required for the vortices to cross them. These had a profound effect on the patterns of vortex order observed which we examine here. Supplementary information can be downloaded from http://www-hrem.msm.cam.ac.uk/people/loudon/#publications
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