The linked fetal globin genes (the Gγ- and Aγ-globin genes) were cloned from Japanese individuals with three different haplotypes of the HindIII polymorphisms within the γ-globin genes. Determination of nucleotide sequences of the segment spanning from IVS2 to the 3' flanking region of each γ-globin gene revealed that nucleotide differences are located at 43 positions and a stretch of simple GT or GC sequences. Almost half of the nucleotide changes could be accounted for by gene conversion between the Gγ- and Aγ-globin genes. We found that gene conversion had created the SacI polymorphic site just downstream of the Aγ-globin coding region. Association of the SacI polymorphic site with the HindIII polymorphic site suggests that the region containing these two sites was derived from that of the linked Gγ-globin gene through a gene conversion event. The nucleotide sequences obtained here are identical to those of the Caucasoid fetal globin genes of the same haplotypes, with the exception of some sequence changes in the hot spots of mutations. These results indicate that the sequence heterogeneity of the γ-globin genes can be classified into three major categories according to HindIII haplotypes. The possible mechanisms of generation of the heterogeneity of the γ-globin gene sequences are discussed.