The Fell and Dales are UK pony breeds that have small populations and may be at risk from in-breeding and inherited diseases. Foal immunodeficiency syndrome (FIS) is a lethal inherited disease caused by the recessive mutation of a single gene, which affects both Fell and Dales ponies and potentially other breeds that have interbred with either of these. FIS, previously known as Fell pony syndrome, is characterised by progressive anaemia and severe B lymphocyte deficiency. The identification of the causal mutation for this disease led to the recent development of a DNA-based carrier test. In this study, the authors used this test to estimate the prevalence of the FIS mutation in the Fell and Dales populations, revealing that approximately 18 per cent of adult Dales ponies and 38 per cent of adult Fell ponies are carriers of the FIS defect. In addition, a study of five potential at-risk breeds was conducted to assess the transfer of the FIS defect into these populations. Of the 192 coloured ponies tested, two were confirmed as FIS carriers: No carriers were found among 210 Clydesdales, 208 Exmoor ponies, 161 Welsh section D, 49 part-bred Welsh section D and 183 Highland ponies.