Some studies have shown that only A2 β-casein–containing milk (A2 milk) causes fewer gut symptoms in milk-sensitive individuals compared with milk containing both A1 and A2 β-caseins (A1A2 milk). However, in most of the previous clinical studies, the role of lactose in symptom generation has been largely overlooked. Partial hydrolysis of β-caseins during milk processing has been noted to influence gastrointestinal symptoms of sensitive individuals, such as those with irritable bowel syndrome. Currently, there is no clear conclusion about the factors behind gut symptoms in milk-sensitive individuals, aside from lactose in those who are lactose intolerant, or milk protein allergy. Our study involved a 3-leg, 3-d randomized crossover trial examining the effects of heat-treated, homogenized A2 and hydrolyzed A1A2 milk on gastrointestinal symptoms, fecal calprotectin, and plasma inflammation markers in 36 self-reported milk-sensitive volunteers. During the result interpretation phase, the participants were categorized into groups according to their lactase enzyme genotype. There was no difference in the amount of perceived gut symptoms between A2 and A1A2 hydrolyzed milk in the lactose-tolerant group, while gut symptoms increased in the lactose-intolerant group along with the increasing lactose content. Calprotectin and high-sensitivity CRP did not increase during any of the intervention periods compared with the milk-free run-in period. Weak evidence of certain inflammatory cytokine changes was seen, but no significant results were obtained. In conclusion, protein-hydrolyzed lactose-free A1A2 milk was as tolerated as A2 milk in lactose-tolerant volunteers and better tolerated by lactose-intolerant volunteers.