Isogeometric analysis (IGA) is a computational methodology recently developed to numerically approximate Partial Differential Equation (PDEs). It is based on the isogeometric paradigm, for which the same basis functions used to represent the geometry are then used to approximate the unknown solution of the PDEs. In the case in which Non-Uniform Rational B-Splines (NURBS) are used as basis functions, their mathematical properties lead to appreciable benefits for the numerical approximation of PDEs, especially for high order PDEs in the standard Galerkin formulation. In this framework, we propose an a priori error estimate, extending existing results limited to second order PDEs. The improvements in both accuracy and efficiency of IGA compared to Finite Element Analysis (FEA), encourage the use of this methodology in the haemodynamic applications. In fact, the simulation of blood flow in arteries requires the numerical approximation of Fluid-Structure Interaction (FSI) problems. In order to account for the deformability of the vessel, the Navier-Stokes equations representing the blood flows, are coupled with structural models describing the mechanical response of the arterial wall. However, the FSI models are complex from both the mathematical and the numerical points of view, leading to high computational costs during the simulations. With the aim of reducing the complexity of the problem and the computational costs of the simulations, reduced FSI models can be considered. A first simplification, based on the assumption of a thin arterial wall structure, consists in considering shell models to describe the mechanical properties of the arterial walls. Moreover, by means of the additional kinematic condition (continuity of velocities) and dynamic condition (balance of contact forces), the structural problem can be rewritten as generalized boundary condition for the fluid problem. This results in a generalized Navier-Stokes problem which can be expressed only in terms of the primitive variables of the fluid equations (velocity and pressure) and in a fixed computational domain. As a consequence, the computational costs of the numerical simulations are significantly reduced. On the other side, the generalized boundary conditions associated to the reduced FSI model could involve high order derivatives, which need to be suitably approximated. With this respect, IGA allows an accurate, straightforward and efficient numerical approximation of the generalized Navier-Stokes equations characterizing the reduced FSI problem. In this work we consider the numerical approximation of reduced FSI models by means of IGA, for which we discuss the numerical results obtained in Haemodynamic applications.