Electron microscope tomography was used to examine the membrane topology of brown adipose tissue (BAT) mitochondria prepared by cryofixation or chemical fixation techniques. These mitochondria contain an uncoupling protein which results in the conversion of energy from electron transport into heat. The three-dimensional reconstructions of BAT mitochondria provided a view of the inner mitochondrial membrane different in important features from descriptions found in the literature. The work reported here provides new insight into BAT mitochondria architecture by identifying crista junctions, including multiple junctions connecting a crista to the same side of the inner boundary membrane, in a class of mitochondria that have no tubular cristae, but only lamellar cristae. Crista junctions were defined previously as the tubular membranes of relatively uniform diameter that connect a crista membrane with the inner boundary membrane. We have also found that the cristae architecture of cryofixed mitochondria, including crista junctions, is similar to that found in chemically fixed mitochondria, suggesting that this architecture is not a fixation artifact. The stacks of lamellar cristae extended through more of the BAT mitochondrial volume than did the cristae we observed in neuronal mitochondria. Hence, the inner membrane surface area was larger in the former. In chemically fixed mitochondria, contact sites were easily visualized because the outer and inner boundary membranes were separated by an 8 nm space. However, in cryofixed mitochondria almost all the outer membrane was observed to be in close contact with the inner boundary membrane.