Inbreeding has the potential to negatively impact on animal performance. Strategies to monitor and mitigate inbreeding depression require that it can be estimated accurately. Here, we use genome-wide SNP data to produce three alternative estimates of inbreeding: proportion of heterozygous SNP, diagonal elements of the genomic relationship matrix and runs of homozygosity. We focus on Brahman (N = 2,112) versus Tropical Composite (N = 2,550) cattle which have been genotyped by a 74K Indicine chip and phenotyped for 10 traits of commercial importance to tropical adaptation. While the summary statistics for the Brahman and Tropical Composite populations are remarkably similar, the relationships of the inbreeding coefficients to the various phenotypes are different. In both populations, the proportion of heterozygous SNP was positively correlated with body condition score and negatively correlated with yearling weight. A possible explanation relating to the content of the Indicine SNP chip is briefly discussed.