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The wild diversity of the Coffea genus is large, which is valuable for coffee plant breeding programs intended to obtain higher sensory quality varieties; but a biochemical characterization of accessions, already available in coffee germplasm banks, is still needed. In this work, a quantitative determination of caffeine, trigonelline and 5-caffeoylquinic acid (5-CQA), in coffee leaves of 80 different Coffea spp. accessions from the Coffee Germplasm Bank located in Huatusco, Veracruz, Mexico was done. These metabolic variables might be useful as quality-related selection markers in future coffee breeding programs. Fresh coffee leaves from each accession were processed and metabolites determined by UPLC-MS/MS analyses. Multidimensional Scaling (MDS), Hierarchical Cluster Analysis (HCA) and Analysis of Variance (AOV) revealed that levels of caffeine and trigonelline in leaves significantly varied among accessions, from 0.00 to 2.04% (w/w) and from 0.42 to 1.82% (w/w), respectively. While 5-CQA ranged from 0.00 to 0.66%. In C. liberica no caffeine was detected, demonstrating that coffee leaves have the potential to be used in the genetic profiling of Coffea spp. These results could be useful in formulating a proposal for intraspecific crosses in C. arabica, for the generation of F1 hybrids with good cup quality attributes, while in C. canephora they could be helpful for enhancing sensory quality traits of Robusta coffees. [ABSTRACT FROM AUTHOR]