Cows managed for extended lactations of 16 months duration were milked on a half-udder basis twice or thrice daily, commencing in lactation week 9. Mammary epithelial integrity (assessed by milk sodium[ratio ]potassium ratio) was greater in the half-udder which was milked thrice daily. This difference was evident throughout the lactation but became greater after week 41. Milk protein composition was assessed during late lactation (52±3 weeks). Casein number (casein as a proportion of total protein) was significantly higher in half-udders milked thrice daily, as were the relative amounts of α- and β-caseins, whilst those of κ- and γ-caseins were reduced. Two days of inverted milking frequency (i.e. thrice-milked udder halves now milked twice, and vice versa) only partly reversed these differences. We concluded that thrice-daily milking will help to prevent or ameliorate the usual decline in milk processing quality associated with late lactation. Part of this effect is due simply to reduced exposure to proteolytic enzymes as a result of decreased storage time in the udder, but part is due to a better maintenance of epithelial tight junction integrity as lactation advances, which restricts leakage of proteolytic enzymes from serum into milk.