Our objective was to analyze the changes in fatty acid (FA) profiles of bovine colostrum and immature milk during the first four days of lactation and assess their potential impact on human health. Colostrum and immature milk samples were collected from Czech Fleckvieh cows during their first to third lactation and the FA profiles were analyzed using multidimensional gas chromatography with a vacuum ultraviolet detector (GC×GC-VUV). The colostrum of primiparous cows contained lower levels of medium-chain and saturated fatty acids, and higher levels of mono- and unsaturated fatty acids compared to that of multiparous cows. The atherogenic and thrombogenicity indexes, as well as the hypocholesterolemic-to-hypercholesterolemic fatty acid ratio, were more favourable in primiparous cows. This makes colostrum fat an attractive product for human nutrition. To obtain the maximum health benefits, we recommend collecting and processing the colostrum of primiparous cows and immature milk at the end of the milk transition separately.