Domestication of wild animals results in a reduction in the effective population size and this could affect the deleterious mutation load of domesticated breeds. Furthermore, artificial selection will also contribute to accumulation deleterious mutations due to the increased rate of inbreeding among these animals. The process of domestication, founder population size, and artificial selection differ between cattle breeds, which could lead to a variation in their deleterious mutation loads. We investigated this using the whole genome data from 432 animals belonging to 54 cattle breeds of the world. Our analysis revealed a negative correlation between the genomic heterozygosity and the ratio of amino acid changing diversity to silent diversity. This suggests a proportionally higher amino acid changing Single Nucleotide variants (SNVs) in breeds with low diversity. Our results also showed that breeds with low diversity had more high-frequency (DAF > 0.51) deleterious SNVs than those with high diversity. A reverse trend was observed for the low-frequency (DAF ≤ 0.51) deleterious SNVs. Overall, taurine cattle breeds had more high-frequency deleterious SNVs than indicine (or taurine-indicine hybrid) breeds. However, within taurine breeds European or Northeast Asian taurines had more high-frequency deleterious SNVs than East Asian or African taurine breeds. Similarly, within indicine breeds South Asian indicines had more high-frequency deleterious SNVs than East Asian indicine breeds. All the above observed patterns were reversed for low frequency deleterious SNVs. Some of the variation in the deleterious mutation load observed between different breeds could be attributed to the population sizes of the wild progenitors before domestication. However, the variations observed withing taurine and within indicine breeds could be due to the difference in the extent of inbreeding, strength of artificial selection and/or founding population size. The findings of this study imply that the rate of incidence of genetic diseases might vary between cattle breeds.