The aims of this study were to: (1) determine whether replacement of cow's milk protein with soy resolves Chronic Functional Constipation (CFC); and (2) investigate the effects of cow's milk β casein A1 and cow's milk β casein A2 on CFC. Children diagnosed with CFC were recruited to one of two crossover trials: Trial 1 compared the effects of cow's milk and soy milk; Trial 2 compared the effects of cow's milk β casein A1 and cow's milk β casein A2. Resolution of constipation was defined as greater than eight bowel motions during a two week intervention. Thirteen children (18 to 144 months) participated in Trial 1 (6 boys, 7 girls). Nine participants who completed the soy epoch all experienced resolution (p < 0.05). Thirty-nine children (21 to 144 months) participated in Trial 2 (25 boys, 14 girls). Resolution of constipation was highest during the washout epoch, 81%; followed by cow's milk β casein A2, 79%; and cow's milk β casein A1, 57%; however, the proportions did not differ statistically. The results of Trial 1 demonstrate an association between CFC and cow's milk consumption but Trial 2 failed to show an effect from type of casein. Some other component in cow's milk common to both A1 and A2 milk may be causing a problem in these susceptible children.