Background We investigated whether the CYP2C9 genotypes would affect lornoxicam metabolism in healthy volunteers. Methods Twelve healthy volunteers who had been genotyped for CYP2C9 gene were selected to participate in our study. After 8 mg lornoxicam was taken, blood samples were drawn from 0 to 36 h. The plasma concentrations of lornoxicam and 5′-hydroxylornoxicam were determined by HPLC method. 5′-hydroxylornoxicam was purified from rabbits'urine by semi-preparative HPLC. Results Lornoxicam and 5′-hydroxylornoxicam both exhibit CYP2C9 genotype-dependent pharmacokinetic profiles. The area under the plasma concentration–time curve (AUC) of lornoxicam increased by 60 ± 9.78% ( P < 0.05) and the AUC of 5′-hydroxylornoxicam decreased by 65 ± 11.75% ( p < 0.001) in heterozygous CYP2C9*1/*3 subjects ( n = 6) compared with CYP2C9*1/*1 group ( n = 6). t 1 / 2 value of lornoxicam and 5′-hydroxylornoxicam prolonged by 39 ± 8.35% and curtailed by 59 ± 6.83% respectively in CYP2C9*1/*3 subjects. But no significant differences in T max of lornoxicam and 5′-hydroxylornoxicam were observed between these 2 genotypes. In addition, for the first time we exploit the purification method for 5′-hydroxylornoxicam from rabbits' urine. Conclusion The CYP2C9*3 allele significantly affected the metabolism of lornoxicam. The pharmacokinetic parameters of both lornoxicam and 5′-hydroxylornoxicam were significantly different between these 2 genotypes.