Abstract: A study was carried out to characterise thirty-seven Coffea canephora clones using three biochemical characteristics, namely caffeine, phenol and protein content. The phenol and caffeine contents were determined by gravimetric method, while protein was assessed by polyacrylamide gel electrophoresis (PAGE) of floral bud. Caffeine content among the clones ranged from 1.1 to 1.5% on dry matter basis (dmb). C36 a high yielding clone, had relatively low caffeine content, hence it is a suitable clone that could be included in any breeding programme for low caffeine coffee in Nigeria. All the Niaollou (M) clones had high caffeine content. Phenol content in the berry pulp of the clones ranged from 2.6 to 15.6%. Averaged over clones, phenol content of berry pulp (9.5 %) was significantly (P < 0.05) higher than leaf phenol content (4.5 %). The coefficient of variation for pulp phenol was high (35.3), thus indicating that, rapid response to selection for favourable phenol percentage might be feasible. The high level of phenol found in some clones may be valuable in breeding for resistance to some major diseases and insect pests of coffee. There were differences in the mobility and intensity of protein bands in the clones. The variation in the protein banding patterns of the different C. canephora clones observed provides further information on the existing genetic diversity of the coffee clones in addition to that provided by agro-botanical characters.