Genetic analyses were conducted on alkaline phosphatases of the endosperm of dry kernels and leaf acid phosphatases in four open pollinated and one inbred line of cultivated rye (Secale cereale L.). A total of seven alkaline phosphatase isozymes were observed occurring at variable frequencies in the different cultivars analyzed. We propose that at least five loci control the alkaline phosphatases of rye endosperm - Alph-1, Alph-2, Alph-3, Alph-4 and Alph-5 - all of which have monomeric behaviour. The leaf acid phosphatases are controlled by one locus and have a dimeric quaternary structure. All loci coding for alkaline phosphatase isozymes showed one active, dominant allele and one null, recessive allele, except for the locus Alph-3 which showed two active, dominant alleles and one null, recessive one. The linkage analyses suggest the existence of two linkage groups for alkaline phosphatases: one of them would contain Alph-2, Alph-4, Alph-5 and the locus/loci coding isozymes 6 and 7. This linkage group is located in the 7RS chromosome arm. The other group would include Alph-1 and Alph-3 loci, being located in the 1RL chromosome arm. Leaf acid phosphatases have been previously located in the 7RL chromosome arm. Our data also support an independent relationship between loci controlling the endosperm alkaline phosphatases and leaf acid phosphatases.