During coffee roasting process, several substances may be formed or eliminated. The influence of roasting on polycyclic aromatic hydrocarbons (PAHs), caffeoylquinic acids (CQAs) and caffeine levels was studied in Coffea arabica cv. Catuaí Amarelo IAC-62 and Coffea canephora cv. Apoatã IAC-2258, roasted in three roasting degrees. CQAs and caffeine were determined simultaneously by HPLC-DAD, and PAHs by HPLC-FLD. Caffeine levels were higher in canephora (1486–1884 mg per 100 g) than in arabica (1110–1255 mg per 100 g) and increased up to 21% at darker roasts. Summed CQA levels were higher in green coffee (4661 and 4946 mg per 100 g) and decreased at darker roasts (234 and 377 mg per 100 g), showing no difference between the coffee cultivars studied. PAH summed levels varied from 0.052 to 0.814 μg kg−1 (arabica) and 0.108 to 0.392 μg kg−1 (canephora). No correlation was observed between roasting degree, coffee cultivar and PAH levels. Results were also analysed using hierarchical cluster analysis and principal component analysis.