Domestic cats are not only a popular and beloved household pet, but also increasingly attracting attention within the scientific community as potential model organism for human hereditary and infectious diseases. Understanding genetic diseases in cats is central to the maintenance of healthy pets and has the potential to be used as a medical model for humans. In this era of genome-wide studies, insights about linkage disequilibrium (LD) are essential for successful association mapping. The objective of this study is to investigate the extent of LD in the domestic cat Felis catus, particularly within its breeds. To finely estimate LD in different populations, a custom Illumina GoldenGate Assay was developed for the domestic cat. The assay consisted of 1536 SNPs equally divided over 10 chromosomal regions. Approximately, 150 SNPs were distributed over a contiguous 1Mb region of each chromosome to allow detection of LD variation. Eighteen globally recognized cat breeds and two distinct random bred populations were selected for the analysis. Two LD descriptive measures (r2 and D`) were calculated pair-wise between the SNPs in each region and each population independently. LD decay was estimated by finding the non-linear least-squares of the pair-wise estimates as a function of distance. LD decay is fastest in random bred populations and varied across breeds. Significant LD in breeds ranged between several hundred kilobases to beyond 1Mb. Measures of LD in breeds reflect the recent breeding history, the small population size, and the levels of inbreeding.