Mitochondria are the main producers of the cellular fuel (adenosine triphosphate, ATP) that eukaryotes require to function. Understanding mitochondrial biology and pathology is therefore important when enquiring about the evolution of animal form and function. Mitochondrial measurement often involves invasive, or even terminal, sampling, which can be difficult to reconcile in wild models or in longitudinal studies. Non-mammal vertebrates contain mitochondria in their red blood cells. This has recently been exploited for minimally invasive mitochondrial measurement in a range of bird species. Studies to date have measured mitochondrial function using isolated blood cells. This is time consuming and might result in technical complications if extended handling of blood cells impacts their integrity. Interpretation of homogenate measurement can also be problematic on biological grounds since homogenate production eliminates biological tissue context. We developed a protocol to measure mitochondrial respiration in bird whole blood samples. Endogenous respiration was comparable between isolated blood cells and whole blood. However, respiration towards oxidative phosphorylation (whereby ATP is produced) was higher in whole blood. Moreover, whole blood mitochondria were better coupled and had higher maximum working capacity, as well as higher and more precise repeatability, compared to cell isolates. Whole blood measurement was feasible over a 10-fold range of sample volumes, though changes to respiratory traits were recorded for both very small and very large samples. We found that the blood can be stored for extended periods of time. After 24 h at 5 degrees C without agitation all respiration traits but maximum working capacity remained unchanged, the latter decreasing by 14%. Finally, we provide proof of principle that whole blood samples, like isolated hematocytes, can be quickly and reliably permeabilised. Our study indicates that measurement of whole blood can provide faster, more precise, and more biologically (tissue context) and physiologically (mitochondrial integrity) relevant assessment of mitochondrial respiration in bird blood cells. On these grounds, we recommend future studies to take a whole blood approach unless specific circumstances require the use of isolated blood cells.