Barn owl pellet content was studied on seven occasions over a 2-y period during which terrestrial small-mammal populations were assessed via a capture-mark-recapture (CMR) programme in a Sahelian agro-ecosystem of the Inner Delta of Niger River in Mali. Rodents (especially Mastomys huberti representing 78.5% of the total number of prey) were the major prey of the barn owl on all but one occasion, when bats were dominant. This exception coincided with the period of lowest abundance of M. huberti at the study site. Distribution of M. huberti prey into four age classes was assessed through analysis of tooth wear in remains from the seasonal pellet samples. Comparisons with age structure of the CMR population indicate that the barn owl tended to prey on smaller-than-average (thus younger) individuals, especially when these are rare in the population (non-reproductive period between June and October). The spectrum of prey consumed is compared with data previously reported in Sahelian Africa, showing for the first time in this region a major shift in prey choice by the barn owl when its preferred prey becomes rare. At the rodent population level, the apparent choice of younger M. huberti prey at some periods is interpreted in the light of our knowledge on population dynamics of the species in this habitat.