The European rabbit Oryctolagus cuniculus is a key species in Mediterranean ecosystems of the Iberian Peninsula, and reliable methods for monitoring its abundance are urgently required. Although clearance plot pellet counts may be useful in monitoring rabbit populations, such counts are potentially affected by variation in the persistence of rabbit pellets. The aim of our study was to assess persistence of rabbit pellets in the Iberian Peninsula for reliable estimates of rabbit abundance from clearance plot counts. We carried out the experiment from July 2006 to November 2007 at seven localities in central southern Spain. Marked fresh pellets were monthly placed at experimental plots, and their persistence was monitored monthly. Persistence was estimated from the proportion of marked pellets remaining between consecutive counts. Independent variables in analysis included slope steepness, vegetation, rabbit and ungulate activity, meteorology and temporal variables. Persistence significantly varied among localities and seasons and with their interaction. The final model showed that pellet persistence was best explained by total rainfall between counts, and also included the time between visits and slope steepness and the interactions rainfall*time between visits and rainfall*slope. Our results suggest that estimating pellet persistence for each locality and season is necessary to make estimates obtained from different localities and months comparable. In the Mediterranean region, early summer at the start of the dry season would be the recommended time for yearly rabbit monitoring based on any pellet-count index, since reduced rainfall favours pellet persistence. Sampling protocols must standardise the number of days between counts, and plots must be established in areas with gentle slope to maximise pellet persistence between counts.