New Findings r What is the central question of this study?The assessment of Ca 2+ handling by isolated mitochondria can be biased by dysfunctions secondary to Ca 2+ -induced mitochondrial permeability transition (MPT). As a result of this uncertainty and the differing experimental conditions between studies, the tissue and sex diversities in mitochondrial Ca 2+ transport are still unsettled questions. r What is the main finding and its importance?If MPT is not prevented during Ca 2+ transport assays, some measured variables are biased. Accounting for the implied importance of preventing MPT, we observed substantial tissue specificities in the mitochondrial Ca 2+ handling, particularly in the Ca 2+ efflux pathways.The characteristics of mitochondria, including their Ca 2+ transport functions, may exhibit tissue specificity and sexual dimorphism. Given that measurements of Ca 2+ handling by isolated mitochondria may be biased by dysfunction secondary to Ca 2+ -induced mitochondrial permeability transition (MPT) pore opening, this study evaluated the extent to which MPT inhibition by ciclosporin affected the measurement of Ca 2+ transport in isolated rat liver mitochondria. The results indicate that the steady-state levels of external Ca 2+ and the rates of mitochondrial Ca 2+ efflux through the selective pathways can be overestimated by up to fourfold if MPT pore opening is not prevented. We analysed Ca 2+ transport in isolated mitochondria from the liver, skeletal muscle, heart and brain of male and female rats in incubation conditions containing MPT inhibitors, NAD-linked substrates and relevant levels of free Ca 2+ , Mg 2+ and Na + . The Ca 2+ influx rates were similar among the samples, except that the liver mitochondria displayed values fourfold higher. In contrast, the Ca 2+ efflux rates exhibited more tissue diversity, especially in the presence of Na + . Interestingly, the Na + -independent Ca 2+ efflux was highest in the heart mitochondria (ß4 nmol mg −1 min −1 ), thus challenging the view that cardiac mitochondrial Ca 2+ efflux relies almost exclusively on a Na + -dependent pathway. Sex specificity was observed in only two kinetic indexes of heart mitochondrial Ca 2+ homeostasis and in the ADP-stimulated respiration of liver mitochondria (ß20% higher in females). The present study