The POINT-AGAPE collaboration has been monitoring M31 for three seasons with the Wide Field Camera on the Isaac Newton Telescope. In each season, data are taken for one hour per night for roughly sixty nights during the six months that M31 is visible. The two fields of view straddle the central bulge, northwards and southwards. We have calculated the locations, periods and amplitudes of 35414 variable stars in M31 as a by-product of our microlensing search. The variables are classified according to their period and amplitude of variation. They are classified into population I and II Cepheids, Miras and semi-regular long-period variables. The population I Cepheids are associated with the spiral arms, while the central concentration of the Miras and long-period variables varies noticeably, the stars with brighter (and shorter) variations being much more centrally concentrated. A crucial role in the microlensing experiment is played by the asymmetry signal. It was initially assumed that the variable stars would not be a serious problem as their distributions would be symmetric. We demonstrate that this assumption is not correct. We find that differential extinction associated with the dust lanes causes the variable star distributions to be asymmetric. The size and direction of the asymmetry of the variable stars is measured as a function of period and amplitude of variation. The implications of this discovery for the successful completion of the microlensing experiments towards M31 are discussed. (Abridged)