The effects of various hydroxide compounds on base stacking (BS) were investigated for pre-concentration of DNA molecules in capillary electrophoresis (CE). In BS, hydroxide ions ($OH^-$) were electrokinetically introduced after DNA sample injection. A neutralization reaction occurred between the $OH^-$ and $Tris^+$ of the running buffer, which resulted in a zone of lower conductivity. Within the low conductivity zone of the high electric field, the DNA molecules moved more rapidly and were concentrated in front of the low conductivity zone. At the same BS conditions of CE, the enhanced sensitivity of the DNA samples was dependent on the kind of multivalent cations in the hydroxide compounds. Except for LiOH, the hydroxide compounds with monovalent cations showed more effective BS than those with divalent cations because of solubility, ionic strength and electronegativity. The order of hydroxide compounds that enhance the detection sensitivity of DNA molecules was as follows: NaOH > $NH_4OH$ > KOH > $Ba(OH)_2$ > $Sr(OH)_2$ > LiOH > $Ca(OH)_2$ > $Mg(OH)_2$. $NH_4OH$, KOH and $Ba(OH)_2$ proved to be efficient hydroxide compounds to use as effective BS reagents in CE instead of NaOH.