In this paper we present a catalogue of Giant Molecular Clouds (GMCs) in the Andromeda (M31) galaxy extracted from the Hershel Exploitation of Local Galaxy Andromeda (HELGA) dataset. GMCs are identified from the Herschel maps using a hierarchical source extraction algorithm. We present the results of this new catalogue and characterise the spatial distribution and spectral energy properties of its clouds based on the radial dust/gas properties found by Smith et al (2012). 236 GMCs in the mass range 10^4-10^7 M_sol are identified, their cumulative mass distribution is found to be proportional to M^-1.45 in agreement with earlier studies. The GMCs appear to follow the same cloud mass to L_CO correlation observed in the Milky Way. However, comparison between this catalogue and interferometry studies also shows that the GMCs are substructured below the Herschel resolution limit suggesting that we are observing associations of GMCs. Following Gordon et al. (2006), we study the spatial structure of M31 by splitting the observed structure into a set of spiral arms and offset rings. We fit radii of 10.5 and 15.5 kpc to the two most prominent rings. We then fit a logarithmic spiral with a pitch angle of 8.9 deg to the GMCs not associated with either ring. Lastly, we comment upon the effects of deprojection on our results and investigate the effect different models for M31's inclination will have upon the projection of an unperturbed spiral arm system. ; Comment: Submitted to ApJ, 21 figures; rev v2 to correct cross-references (resub: update to series numbering)