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The objective of this open-label, single-dose study was to clarify the influence of the menstrual cycle on the pharmacokinetics of theophylline (n = 10) and amikacin (n = 8) in young healthy Japanese women with regular menstrual cycles. Each subject received an intravenous infusion of theophylline or amikacin sulfate at four different phases—mid-follicular (phase I), peri-ovulatory (phase II), mid-luteal (phase III), and premenstrual days (phase IV). In the theophylline study, there were no significant differences in the pharmacokinetic parameters among the four phases studied. In the amikacin study, CLtot was 15% higher in phase III than in phase I (p < 0.01). Vdβ was 35% higher in phase III than in phase I (p < 0.05). The other pharmacokinetic parameters of amikacin were not significantly altered during the menstrual cycle. Evidence suggests that the phase of the menstrual cycle maybe a factor in determining the pharmacokinetics of amikacin.