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An environmentally friendly analytical procedure of pre-concentration of cobalt, nickel, and copper according to the rules of green chemistry has been developed. The proposed method is based on using chitosan for sorption of trace elements from water samples. The novel modification of the sorption process is the combination of an ionic liquid (1-butyl-3-methylimidazolium hexafluorophosphate [BMIM][PF6]) with chitosan. Ionic liquid partly decreases the crystallinity of the chitosan. The crystalline regions of the polymer are not accessible to metal ions. Although the ionic liquid cannot completely disrupt the crystalline domains of chitosan, it may gain in the reactive groups of the chitosan, even at the center of the particle. Consequently, the sorption of metal ions by chitosan is significantly improved. In this paper, adsorption characteristics of cobalt, nickel, and copper using newly developed sorption are studied. The effect of pH and time of chitosan activation, as well as sorption, salt concentration, some metals ion concentrations, and the amount of adsorbent on the extent of adsorption, are investigated. Chitosan with adsorbed metal ions was dissolved in acetic acid. After evaporation a solvent film formed and was then analyzed using X-ray fluorescence spectrometry (XRF). As it meets the criterion of thin samples for XRF analysis, the matrix effects can be neglected. With the proposed procedure we obtained detection limits of 7 ng mL−1for cobalt, 5 ng mL−1for nickel, and 4 ng mL−1for copper. [ABSTRACT FROM AUTHOR]