Ten polymorphic systems of blood antigens and blood proteins were analyzed in 6,802 Guernsey cows from 77 herds and 11 states. The numbers of alleles identified with frequencies > 1% in the A, B, C, F, J, L, M, S, and Z blood antigen systems and the alkaline phosphatase system were 3, 17, 11, 2, 2, 2, 1, 3, 2, and 2. Gene frequencies were determined by maximum likelihood, allocation, and square root methods for the dominant systems and by the gene counting method for the codominant system. Distributions varied greatly in the different systems. Comparisons among these and other blood and milk genetic marker systems revealed lack of independence of J and alkaline phosphatase phenotypes, J and milk protein beta-lactoglobulin phenotypes, and of combined phenotypes of the three systems. More cows than expected were J-negative when alkaline phosphatase A was present or when beta-lactoglobulin B was present. Phenotypes of blood antigen system A and hemoglobin were also different from independent assortment. More hemoglobin B cows had blood antigen system A phenotype A than the other phenotypes. The blood antigen locus F had more heterozygous cows than were expected for Hardy-Weinberg equilibrium.