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.In both cases, Λ + = ∅. Thus we obtain a new proof of the following result.Corollary 1.4 ([23]). If Λ ⊂ P × R admits an augmentation, then there is no exact Lagrangian cobordism from Λ to ∅, i.e. there is no exact Lagrangian "cap" of Λ.Remark 1.5. Assume that Λ − admits an exact Lagrangian filling L inside the symplectisation, and that ε − is the augmentation induced by this filling. It follows that ε + is the augmentation induced by the filling L ⊙ Σ of Λ + obtained as the concatenation of L and Σ. Using Seidel's isomorphismsto replace the relevant terms in the long exact sequences (1) and (3), we obtain the long exact sequence for the pair (L ⊙ Σ, L) and the Mayer-Vietoris long exact sequence for the decomposition L ⊙ Σ = L ∪ Σ, respectively. This fact was already observed and used by the fourth author in [49].