In the last decades, many progress has been made in our understanding of kidney metabolism and transport of a wide amount of solutes. The purpose of this review is to highlight some issues of kidney metabolism which are still not completely understood and that are nonetheless implicated in the pathophysiology of chronic kidney disease. These untold stories include the recently discovered ammonium transporter proteins Rh and the role of ammonium in causing kidney hypertrophy and renal damage; the role of the human kidney methionine metabolism on epigenetics and the effects of accelerated glucose reabsorption in the proximal tubule on tubulointerstitial damage in diabetic nephropathy. These issues have potential clinical applications and can be a starting point for future research in kidney disease.