Variability is a general property of active galactic nuclei (AGN). At X-rays, the way in which these changes occur is not yet clear. In the particular case of low ionisation nuclear emission line region (LINER) nuclei, variations on months/years timescales have been found for some objects, but the main driver of these changes is still an open question. The main purpose of this work is to investigate the X-ray variability in LINERs, including the main driver of such variations, and to search for eventual differences between type 1 and 2 objects. We use the 18 LINERs in the Palomar sample with data retrieved from Chandra and/or XMM-Newton archives corresponding to observations gathered at different epochs. All the spectra for the same object are simultaneously fitted in order to study long term variations. The nature of the variability patterns are studied allowing different parameters to vary during the spectral fit. Whenever possible, short term variations from the analysis of the light curves and UV variability are studied. ; Comment: 49 pages, accepted. arXiv admin note: text overlap with arXiv:1305.2225