The fragmentation behavior of 18 chlorogenic acids that are not substituted at position 1 has been investigated using LC-MS(4) applied to a methanolic coffee bean extract and commercial cider (hard cider). Using LC-MS(3), it is possible to discriminate between each of the three isomers of p-coumaroylquinic acid, caffeoylquinic acid, feruloylquinic acid, and dicaffeoylquinic acid, and a hierarchical key has been prepared to facilitate this process when standards are not available. MS(4) fragmentations further support these assignments, but were not essential in reaching them. The distinctive behavior of 4-acyl and 3-acyl chlorogenic acids compared with the 5-acyl chlorogenic acids is a key factor permitting these assignments. The fragmentation patterns are dependent upon the particular stereochemical relationships between the individual substituents on the quinic acid moiety. Fragmentation is facilitated by 1,2-acyl participation and proceeds through quinic acid conformers in which the relevant substituents transiently adopt a 1,3-syn-diaxial relationship. Selected ion monitoring at m/z 529 clearly indicated the presence in coffee of six caffeoylferuloylquinic acid isomers, whereas previously only two or three had been demonstrated. The hierarchical key permitted specific structures to be assigned to each of the six isomers. These assignments are internally consistent and consistent with the limited data previously available.