In this work CE-ESI-MS is proposed for the identification and simultaneous quantification of several ribonucleotide 5-monophosphates in infant formula (IF) samples. The target compounds were adenosine 5-monophosphate, cytidine 5-monophosphate, guanosine 5-monophosphate, uridine 5-monophosphate, and inosine 5-monophosphate. To our knowledge, the application of CE for the determination of these bioactive compounds in IFs has not yet been described. Optimization of the composition of the electrophoretic separation buffer and -mainly- the injection medium was carried out with a view to obtaining the best sensitivity and separation efficiency for the CE-MS coupling. Different sample treatments were assayed and one based on centrifugal ultrafiltration proved to be the simplest and most compatible with CE separation of the analytes and their ionization by the electrospray source. The whole optimized method (centrifugal ultrafiltration treatment prior to CE-MS) was validated according to the 2002/657/EC decision, obtaining a reliable and robust CE-MS method to determine these compounds in IF samples, with LODs between 0.8 and 1.8 g/g (S/N = 3) and recoveries in the 90-106% range.