The αₛ₁-casein A variant protein results from a rare polymorphism in the bovine αₛ₁-casein gene. It is dramatically different from other αₛ₁-caseins in that it has a 13 amino acid (encoded by the entire exon 4 of the αₛ₁-casein gene) deletion, which significantly alters the physico-chemical properties of the protein. Previous work suggested that the deletion is caused by exon 4 skipping during RNA processing and that a T→A transversion mutation at position +6 in the intron 4 splice donor site is responsible for this skipping (Mohr et al. 1994). The current investigation initially focused on the genetic aetiology of variant A animals in an New Zealand herd; it was found that a single base (adenine) deletion, which is different from the previously reported mutation in the αₛ₁-casein gene, occurs at position +4 of the intron 4 splice donor site in these animals. An amplification created restriction site (ACRS) based method has been developed to genotype this variant of calves and bulls. Later work centred on the investigation of aberrant αₛ₁-casein A variant RNA and protein arising from RNA processing perturbations rather than mutations in the coding sequences of the gene per se. Interestingly, it was found that αₛ₁-casein A variant mRNA and protein is actually expressed by all normal cows examined, at 1-5 percent of the level of the normal gene product! In addition, the identification of low levels of exon 17 and exon 4&5 aberrant skipped transcripts beside that of the exon 4 skipping suggests that, under normal circumstances, bovine αₛ₁-casein gene mRNA undergoes multi-exon-skipping during processing. Thus, it is possible that this gene might also express a spectrum of other hitherto unsuspected, truncated, αₛ₁-casein proteins. These studies utilised the sloughed off mammary epithelia cells in milk to characterise the αₛ₁-casein mRNAs. This technique was found to provide an ideal non-invasive approach for both gene expression studies on the mammary gland and as a screening technique for milk protein gene polymorphisms.