A subset of cellular compartments maintain acidic interior environments that are critical for the specific functions of each organelle and for cell growth and survival in general. The pH of each organelle reflects the balance between proton pumping, counterion conductance, and proton leak. Alterations in steady-state organelle pH due to defects in either proton pumping activity or counterion conductance have been suggested to contribute to the pathology of several diseases; however, definitive evidence remains elusive. This review describes recent evidence for the misregulation of organelle pH in the progression of cancer, Dent's disease, and cystic fibrosis.