Some alleles are inherited more frequently than expected from Mendel's rule. This phenomenon, known as transmission ratio distortion (TRD), is found in a broad variety of taxa, but it is thought to be unusual and occurs at a low frequency in any particular population. Here, we used seven microsatellite markers to search for possible TRD in a wild lesser kestrel (Falco naumanni) population. Among the nine alleles analysed with at least 200 known meioses for each sex, we found that two of them (156-AG5 in males and 362-FN1.11 in females) presented subtle (k=0.6) but significant departures from Mendelian segregation. Moreover, in a sample of 53 alleles with at least 15 known meioses, we found a positive correlation between their transmission rates and their frequencies in the population. To estimate the transmission scores for the loci and individuals, we developed a method that allowed us to discover that another locus, FP-46, showed significant TRD, despite the lack of a significant deviation from parity for the alleles considered individually. Finally, we found a consistent transmission bias both within loci and within individuals across loci. Inter-individual differences in TRD support the idea that distorters act over several loci that are evenly distributed across the whole genome, particularly in individuals bearing the distorter alleles. Overall, these findings suggest that TRD might be a more widespread phenomenon than previously revealed by analyses at the allele level.