Genetic variants of milk proteins are often overlooked by dairy processors as a parameter that can effect process efficiency. This study assessed the impact of the A and B genetic variants of β-lactoglobulin on the isolation of whey proteins from skim milk by microfiltration. The A and B genetic variants of β-lactoglobulin differ by two amino acids at positions 64 (A = aspartic acid, B = glycine) and 118 (A = valine, B = alanine), with the A variant thus having a higher negative charge. Mass balance calculations indicated that 46.7 % more whey proteins permeated during microfiltration for the A compared to the B variant, with the A also having significantly (P < 0.05) more total and reversible fouling accumulation than the B variant. These findings could be of importance to the dairy industry to improve microfiltration efficiency and increase protein yield during manufacture of native whey protein ingredients.