Forty-five-day-old seedlings of sour orange (Citrus aurantium L.) and Citrus macrophylla Wester, the most commonly used rootstocks in lemon orchards, were grown in nutrient solutions containing 1 (control), 10, 20, 30 or 60 mM NaCl for 14 days. The effects of salinity on growth, uptake, transport and accumulation of Cl- and Na+ ions in leaves, stem and four root segments were studied. The 60 mM NaCl treatment reduced leaf dry mass more in C. macrophylla (40%) than in sour orange (20%), whereas it reduced root dry mass more in sour orange (36%) than in C. macrophylla (20%). In C. macrophylla, Cl- and Na+ uptake rates were high at the beginning of the saline treatments, but low at the end of the 14-day experiment. In contrast, sour orange showed high uptake rates at the beginning and end of the experiment. In response to increasing salinity, root and shoot concentrations of Cl- and Na+ increased in sour orange, but not in C. macrophylla. Different loading characteristics of Cl- and Na+ were observed between young and old segments of the root system. In general, old root segments reached quasi-steady-states later than young root segments. These results suggest that sour orange and C. macrophylla have different regulatory mechanisms for uptake and transport of Cl- and Na+.