The X-ray crystal structures of two self-complementary DNA duplexes with the sequence d(CGCGAAt(Me/OH)t(Me/OH)CGCG) containing four 6’-alpha-methyl (t(Me)) or four 6’-alpha-hydroxy carbocyclic thymidines (t(OH)), respectively, have been determined. Both structures are isomorphous to the native Dickerson-Drew dodecamer duplex [d(CGCGAATTCGCG)](2). The cyclopentane moieties of the modified carbocyclic thymidine residues lacking the deoxyribose 4’-oxygen adopt either C2’-endo or C1’-exo B-DNA type puckers. The dodecamer duplex incorporating 6’-alpha-methyl carbocyclic thymidines shows an enlarged minor groove relative to both the unmodified duplex and the one with incorporated 6’-alpha-hydroxy carbocyclic thymidines. The pairing of oligonucleotides containing single or multiple 6’-alpha-substituted carbocyclic thymidines with complementary DNA is discussed on the basis of the structural data.