Context. One of the most distinctive features in active galactic nuclei (AGN) is the variability of their emission. Variability has been discovered at X-ray, UV, and radio frequencies on timescales from hours to years. Among the AGN family and according to theoretical studies, low-ionization nuclear emission line region (LINER) nuclei would be objects variable on long timescales. Aims: Our purpose is to investigate spectral X-ray variability in LINERs and to understand the nature of these types of objects, as well as their accretion mechanism. Methods: Chandra and XMM-Newton public archives were used to compile X-ray spectra of seven LINER nuclei at different epochs with timescales of years. To search for variability we fit all spectra from the same object with a set of models to identify the parameters responsible for the variability pattern. We also analyzed the light curves to search for short timescale (from hours to days) variability. Whenever possible, UV variability was also studied. Results: We found spectral variability in four objects (NGC 1052, NGC 3226, NGC 4278, and NGC 4552), with variations mostly related to hard energies (2-10 keV). These variations are generated by several possible changes that act either alone or in combination: changes in the soft excess or in the absorber. Added to this can be intrinsic variations of the source, which may also be responsible by themselves for the spectral variability. These variations occurred within years, the shortest timescale being found for NGC 4278 (two months). Another two galaxies (NGC 4261 and NGC 5846) apparently do not vary. No short timescale variations during individual observations were found. Our analysis confirms the previously reported anticorrelation between the X-ray spectral index, Γ, and the Eddington ratio, Lbol/LEdd, and also the correlation between the X-ray to UV flux ratio, αox, and the Eddington ratio, Lbol/LEdd. These results support an advection dominated accretion flow as the accretion mechanism in LINERs. Tables 2-11 and Appendices are available in electronic form at http://www.aanda.org