The HpaI restriction fragment length polymorphism linked to the beta globin gene was studied in 181 Nigerian subjects. The beta s gene was found in the 13 kilobase (kb) HpaI fragment in 98.4 percent and in the remaining 1.6 percent of the cases in the HpaI 7.6 kb fragment. The majority of beta A genes (94.2%) were found in either the 7.6 or the 7.0 kb fragment whilst the remainders (5.8%) were in the 13.0 kb fragment. The rare, but not zero, associations of beta A with the 13 kb linkage and of beta s genes with the 7.6 kb fragment would lessen the accuracy in the prenatal diagnosis of sickle cell anaemia in this population through the use of the HpaI polymorphism.