In the northern Yukon there is a significant group of limestone caves in an area that was not glaciated during the Quaternary. Permafrost appears to have played an important role in restricting calcite speleothem deposition in the caves. U/Th dating and stable isotopic studies indicate that the deposits form two distinct groups, a first group younger than 350 ka, and a second group older than the 350 ka BP limit of the conventional U/Th alpha spectrometric dating method. Two large samples from the second group yield sequences of magnetic declinations and inclinations with reversed and normal polarity, perhaps from the Tertiary. The pollen content of five speleothems, the modes of calcite deposition, and stable isotopic analyses indicate that the speleothems were deposited under a cold regime. It is suggested that the ancient speleothems were deposited at a time when permafrost was absent, during the later Tertiary or at the beginning of the Quaternary period. The establishment and maintenance of permafrost throughout the Quaternary has prevented the formation of younger speleothems, except at a few cave entrances where the active layer may have deepened during interglacials.