The separation/identification of 25 amino acids as their o-phthaldialdehyde–3-mercaptopropionic acid (OPA/MPA) and o-phthaldialdehyde– N-acetyl- l-cysteine (OPA/NAC) derivatives have been optimized [paying particular attention to those amino acids which elute with more than one derivative (glycine, histidine, γ-aminobutyric acid, β-alanine, ornithine, lysine) and that are expected to be present in apples in their free form]. Optimum separation conditions are reported on six reversed-phase columns: Nucleosil 3 and 5 μm, 150(+20 guard)×4.0 mm; Gromsil 3 μm, 150(+10 guard)×4.0 mm; Hypersil 5 μm, 150(+20 guard)×4.0 mm and 200(+20 guard)×4.0 mm; and Hypersil 3 μm, 150(+20 guard)×4.0 mm. Elutions were followed, simultaneously, with photodiode array and fluorescence detectors connected in line. Optimization studies carried out in model solutions as a function of temperature (30–55°C) and eluent flow-rate (0.8–2.5 mL/min) demonstrated that optimum resolutions are obtained with the highest flow-rate applicable (remaining on the safe side with a column pressure of ≪3500 p.s.i.; 1 p.s.i.=6894.76 Pa) in the temperature range 30–50°C. Twenty-five amino acids, eluting in 31 separate, characteristic derivatives, were determined on all six columns (the main component, asparagine, present in overwhelming excess, together with the minor constituents glutamine, β-alanine, γ-aminobutyric acid, homoserine, and homoarginine). Optimum conditions in the case of both derivatives were obtained on the same type of column (Hypersil, 5 μm), as follows: for the OPA/MPA amino acids with programmed flow-rate [1.3–2.3 ml/min; column, 200(+20 guard)×4 mm], at 50°C, while, for the OPA/NAC amino acids at 2.1 ml/min flow rate, at 30°C [column, 150(+20 guard)×4 mm], with 40 and 37 min run times, including equilibration. Responses of the corresponding amino acids proved to be independent of the column used; reproducibility in the concentration range 6–12 000 pmol, related to the injected amount of amino acids, was <3.4% RSD (average relative standard deviation percentage). The utility of the protocol was demonstrated in the quantitation of the free amino acid content of five apple varieties (Jonagored, Idared, Jonica, Florina, Freedom) on various harvesting dates and after different storage times. Derivatization of the apple pulp was performed with filtered samples, applying any special isolation processes.