In this thesis I study various incarnations of rational homotopy theory in the world of arithmetic geometry. In particular, I study unipotent crystalline fundamental groups in the relative setting, proving that for a smooth and proper family of geometrically connected varieties f:X->S in positive characteristic, the rigid fundamental groups of the fibres X_s glue together to give an affine group scheme in the category of overconvergent F-isocrystals on S. I then use this to define a global period map similar to the one used by Minhyong Kim to study rational points on curves over number fields. I also study rigid rational homotopy types, and show how to construct these for arbitrary varieties over a perfect field of positive characteristi...