The potential binding of borate to oligonucleotides and DNA fragments is here investigated. In case of free nucleotides, such as AMP, there appears to be a weak binding, although no free versus complexed species could ever be separated under any experimental condition. The binding was suggested by the strong peak asymmetry and by the fact that, at progressively lower borate molarities in the background electrolyte, the peak shape suddenly switched from fronting to tailing. This indicated, as also confirmed by theoretical simulations, that the AMP-borate complex was the slow, not the fast moving species. On the contrary, in the case of free adenosine, strong binding ensued, since in Tris-acetate buffer this compound was only eluted with the electroendoosmotic flux, being neutral, whereas in Tris-borate it had a much higher mobility, comparable to, although lower than, that of AMP. When running oligonucleotides, at standard borate molarities (ca. 45 mM), and under strict iso-ionic strength conditions, no binding to borate could be demonstrated, since the free mobility of a 24-mer DNA was identical in TA and TB buffers. However, at very high borate molarities (200 mM) and high pH values (pH 8.92), some binding to oligonucleotides could occur, since in these latter conditions the mobility of a 24-mer was seen to be ca. 20% lower than at pH 7.69, a pH value that should discourage any complex formation.