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The goal of conformal radiation techniques is to improve local tumour control through dose escalation to target volumes while at the same time sparing surrounding healthy tissue. Respiratory motion is known to be the largest intra-fractional organ motion and the most significant source of uncertainty in treatment planning for chest lesions. A method to account for the effects of respiratory motion is to use four-dimensional radiotherapy. While analytical models are useful, it is essential that the motion problem in radiotherapy is addressed by both modeling as well as experimentally studies so that different obstacles can be overcome before clinical implementation of a motion compensation method. Validation of techniques aimed at measuring and minimizing the effects of respiratory motion require a realistic dynamic deformable phantom for use as a gold standard. In this work we present the design, construction, performance and deformable image registration of a novel breathing, tissue equivalent phantom with a deformable lung that can reproducibly emulate 3D non-isotropic lung deformations according to any real lung-like breathing pattern. The phantom consists of a Lucite cylinder filled with water containing a latex balloon stuffed with dampened natural sponges. The balloon is attached to a piston that mimics the human diaphragm. Nylon wires and Lucite beads, emulating vascular and bronchial bifurcations, were glued at various locations, uniformly throughout the sponges. The phantom is capable of simulating programmed irregular breathing patterns with varying periods and amplitudes. A deformable, tissue equivalent tumour, suitable for holding radiochromic film for dose measurements was embedded in the sponge. Experiments for 3D motion assessment, motion reproducibility as well as deformable image registration and validation are presented using the deformable phantom.