The major function of the kidney tubule is to transport large amounts of fluid from the glomerular filtrate back into the blood-stream. This imposes high energy demands on tubular cells, which are densely populated with mitochondria to generate sufficient ATP via aerobic metabolism. Transport and metabolism are thought to be tightly coupled in kidney tubules, but the mechanisms via which they are related are poorly understood. Mitochondria are complex and dynamic organelles that have a number of other important functions beyond ATP production. A range of insults can damage mitochondria in kidney tubules – including ischemia, diabetes, toxic drugs and ageing – leading to solute transport defects and progressive declines in kidney function. We have developed live imaging techniques using multiphoton microscopy (MPM) to study the function and behavior of mitochondria in tubular cells in intact kidney tissue, both under physiological conditions and in disease models. Using this approach we have discovered that intrinsic mitochondrial function varies along the nephron, and have made novel insights into mechanisms of mitochondrial dysfunction in kidney tubular diseases.