In this article we define intersection Floer homology for exact Lagrangian cobordisms between Legendrian submanifolds in the contactisation of a Liouville manifold, provided that the Chekanov-Eliashberg algebras of the negative ends of the cobordisms admit augmentations. From this theory we derive several long exact sequences relating the Morse homology of an exact Lagrangian cobordism with the bilinearised contact homologies of its ends.
These are then used to investigate the topological properties of exact Lagrangian cobordisms.