Reaction of [(dach)Pd(NO₃)₂] entities (dach = (R,R)-1,2-diaminocyclohexane, (S,S)-1,2-diaminocyclohexane) and 4,7-phenanthroline (phen) providing, respectively, 90 and 120° bond angles, leads to the formation of two novel positively charged homochiral cyclic trinuclear metallacalix[3]arene species [((R,R)-1,2-diaminocyclohexane)Pd(phen)]₃(NO₃)₆ (2a) and [((S,S)-1,2-diaminocyclohexane)Pd(phen)]₃(NO₃)₆ (2b). These species have been characterised by ¹H NMR and X-ray diffraction methods (2b), showing that they possess accessible cavities suited for supramolecular recognition processes. We prove, indeed, from ¹H NMR studies the inclusion of mononucleotides inside the cavity of the trinuclear species [(ethylenediamino)Pd(phen)]₃⁶⁺ (1), [((R,R)-1,2-diaminocyclohexane)Pd(phen)]₃⁶⁺ (2a) and [((S,S)-1,2-diaminocyclohexane)Pd(phen)]₃⁶⁺ (2b) in aqueous solution. Association constants (K_ass) range from 85 ± 6 M⁻¹ for the interaction between [(ethylenediamine)Pd(phen)]₃⁶⁺ and adenosine monophosphate to 37 ± 4 M⁻¹ for the interaction between [(1,2-diaminocyclohexane)Pd(phen)]₃⁶⁺ and thymidine monophosphate. We invoke the synergy of electrostatic, anion–π and π–π interactions to explain the recognition of mononucleotides inside the cavity of the metallacalix[3]arenes.