Bovine milk is one of the leading causes of childhood food allergies. Alpha-S1-casein (aS1CN) is a significant allergen and the most abundant protein in bovine milk. In contrast, many Swedish Landrace goats have been reported to have a mutation that prevents the production of aS1CN in milk. In this study, quantitative analysis of bovine and caprine aS1CNs was performed using liquid chromatography/tandem mass spectrometry (LC/MS/MS), measuring a shared proteotypic peptide (YLGYLEQLLR) between these proteins. The concentration of caprine aS1CN in caprine milk was significantly (P < 0.01) lower than that of bovine aS1CN in bovine milk. Similarly, in comparison between bovine and caprine milk powders, caprine aS1CN showed a considerably lower content than bovine aS1CN. Although substantially lower than bovine aS1CN, caprine aS1CN was detected in all caprine milk and milk powders.