The electron impact ionisation (EI) and electrospray ionisation (ESI) mass spectra using in-source collision-induced dissociation of nine different cinchona alkaloid derivatives [iso-cinchona alkaloids (ethereal isomers) and 10-Br(Cl) containing cinchona compounds] have been studied. In the case of the EI method for iso-cinchona alkaloids the observed fragmentation directions are as follows: isomerisation of the cyclic ethers to the corresponding C9 ketone, the formation of [M-15] + , [M-29] + and [M-57] + fragments as a result of the loss of methyl, ethyl and butyl radicals, and the cleavage of the C8-C9 bond. The fragmentation of the compounds containing C10-Br(Cl) bonds started with the scission of this bond. The primary bond rupture is followed by the fragmentation of the primary product into two parts across the C8-C9 bond. In the case of the ESI method at low capillary exit voltage only the peak of the protonated molecule ([M + H] +), and in a significantly lower abundance, the peak of the [M + 2H] 2+ ion can be observed. Increasing the capillary exit voltage causes fragmentation to occur. For iso-cinchona alkaloids the main direction is the cleavage of C8-C9 bond. For the C10-Br(Cl) compounds, the primary fragmentations are the cleavage of the C9-O and C10-Br(Cl) bonds. Fragmentation pathways are discussed.