The DNA base lesion spiroiminodihydantoin (Sp) is produced in biological systems endogenously and can cause mutation and cancer. It is considered to be more mutagenic and deleterious than 8-oxoguanine and other oxidized guanine products such as guanidinohydantoin (Gh) and imidazolone. In this work, the base pairing patterns of Sp with each of the normal nucleic acid bases of DNA have been investigated thoroughly using the B3LYP, M06-2X, and wB97X-D functionals of density functional theory in conjunction with the aug-cc-pVDZ basis set. It is found that the magnitudes of interaction energies between the bases and Sp follow the order: Sp-guanine >> Sp-cytosine > Sp-adenine > Sp-thymine. The strong Sp-guanine abnormal base pairing may be the main cause of the observed mutagenicity of Sp. © 2013 Wiley Periodicals, Inc.