ABSTRACT This work focuses on the separation of oligonucleotides (ONs) in a free solution by capillary electrophoresis—mass spectrometry (CE‐MS). Specifically, we evaluated a combination of separation in acidic background electrolytes (BGEs), nanospray ionization, and time‐of‐flight mass spectrometry in positive mode. A mixture of synthetic ONs, ranging in length from 15 to 78 nt, was employed as the test compounds. The key to a good separation selectivity of ONs lies in the different protonation of individual nucleobases. To this end, we assessed the acidity constant (p K a ) of the nucleobases in nucleotides experimentally as 3.3 for adenine, 4.4 for cytosine, 2.5 for guanine, and < 2 for thymine. From a set of separations in the 2–9 pH range, it was found that optimum peak shape and resolution are achieved in the interval of acidic pH 2–2.5. The BGE can be conveniently composed of either formic acid (FA) or a combination of ammonium hydroxide and FA. Nanospray ionization provided ions with charge numbers ranging from +4 to +8, proportional to the length of the ON. For short sequences, sheath liquid (SL) comprising 0.5%–1% (v/v) FA + 20% (v/v) methanol was sufficient in order to generate ions in positive mode MS, whereas a stronger SL of 5% (v/v) FA + 20% (v/v) methanol was required for longer ON sequences of approximately > 40 nt.