The conformation change of DNA fragments due to divalent counterion condensation onto DNA was investigated by pulse gel electrophoresis, and interpreted by gel models (Reptation and Henry model) and Manning's counterion condensation theory. The measured mobility reductions μ/μ0 of λ-DNA-Hind III fragments, ranging from 23.13 to 2.027 kilobase pairs, due to interaction with divalent cation Mg2+ (1–400 μμ), and Ca2+(0–40 μM) in tris-borate buffer were well fit by Manning's Counterion Condensation (CC) theory. We observed the normalized mobility reduction to be shifted by a small amount Δ(μ/μ0) relative to the CC prediction value. Δ(μ/μ0) is a function of DNA length, and the ion environment (divalent concentration C2 and ionic strength). The ‘shift’ phenomena only occurred close to where C2 began dominating the counterion binding, a condition described by the monovalent/divalent cation isocompetition point. Combining our observation with theoretical considerations, we conclude that the divalent counterion condensation changes the DNA fragments' conformation, resulting in an end-to-end distance decrease which is molecular weight dependent. The effect was enhanced by an increase of divalent ion concentration and a decrease of the ionic strength.