Twenty-four dairy goats were used in a preliminary trial to evaluate the effect of the genotype for alpha S1-casein (alpha S1-CN) in milk [homozygous variant A/A (n = 12) or F/F (n = 12)] on milk yield and composition for 2 wk from kidding. After this period, the main trial aimed at determining the effects of the genotype for alpha S1-CN in milk, the dietary crude protein concentration on milk yield and composition, and utilization of N, Ca and P. The goats within each genotype were allocated to a 3 x 3 Latin square for 14 wk with three crude protein concentrations in the total mixed ration (13.2, 16.8, and 19.8% of dry matter) and three periods (wk 3 to 6, wk 8 to 11, and wk 13 to 16 postpartum) as factors. Balances of N, Ca, and P were determined in the last week of each period. Two wk after kidding, the alpha S1-CN A/A goats had higher percentage and yield of protein and lower body weight than the alpha S1-CN F/F goats. During the main trial, yields of protein and fat, as well as percentages of fat and protein in milk were higher for the alpha S1-CN A/A goats than for the alpha S1-CN F/F goats, independent of dietary CP concentration and period. Efficiency of N digestion for milk N was higher for the alpha S1-CN A/A goats than for the alpha S1-CN F/F goats. Urinary N as a percentage of digested N, and total N excretion expressed relative to milk N were lower for the alpha S1-CN A/A goats than for the alpha S1-CN F/F goats. Neither the apparent absorption of calcium or phosphorus was affected by the genotype for alpha S1-CN. Goats fed the low crude protein diet had lower milk yield and lower yields of fat and protein than those fed the other diets. Increasing dietary crude protein concentration increased urinary N, milk N, and N excretion relative to milk N; it also decreased the efficiency of digested N for milk N. In conclusion, selection of goats with a genetically higher yield of casein and fed with diets formulated to reduce N excretion improves the cheese-making properties of goat milk and reduces concerns about N wastes in the environment.