Despite the growing interest and the potential benefits of idebenone as a repurposed drug for different orphan conditions, data regarding its monitoring are scarce. Our main goal was to report plasma idebenone values in a cohort of Friedreich’s ataxia (FRDA) patients during a long-term follow-up. Taking advantage of this, we also assessed cardiological and neurological status together with idebenone values and genetic background. Long-term follow-up retrospective study in 27 FRDA patients with a disease onset at the paediatric age treated with idebenone by compassionate use. Plasma idebenone was measured by HPLC with electrochemical detection. Median plasma idebenone values increased when doses were increased, but apparently linearity was lost in the highest dose group. Marked intraindividual and interindividual differences were observed among patients. We did not find a consistent positive effect after analysis of paired data at the beginning and the end of the study. We only found a correlation between some cardiological measures and the duration of idebenone therapy at high doses, but with uncertain significance. The large variations observed among the different individuals involved in this study should be considered for optimization of individual dosage regimens. •Despite the growing interest and the potential benefits of idebenone, data regarding its monitoring are scarce.•We report plasma idebenone values of a cohort of 27 Friedreich’s ataxia patients during a long-term follow-up period.•Large interindividual and intraindividual variability in plasma idebenone concentrations was observed.•These large variations should be considered for optimization of individual dosage regimens.