A heat transfer catheter system, comprising: a heat transfer catheter configured for insertion into a patient; a disposable heat exchange unit having a fluid pathway therewithin and incorporating an integral pump head adapted to move fluid through the fluid pathway; conduits coupled to the heat transfer catheter and heat exchange unit adapted to enable circulation of a heat exchange medium therebetween upon operation of the pump head; a diverter unit adapted to periodically redirect the fluid pathway to bypass the heat transfer catheter; a plurality of sensors (58a-b, 80) for providing signals representative of patient data; and a reusable master control unit having a heater/cooler and a pump driver, the disposable heat exchange unit being adapted to couple to the master control unit such that the pump driver engages the integral pump head and so that the fluid pathway is in thermal communication with the heater/cooler, the master control unit also having a microprocessor configured to receive the signals representative of the patient data from the plurality of sensors (58a-b, 80) and to control the heater/cooler in accordance with the signals received from the plurality of sensors, the microprocessor further configured to receive a target temperature input and wherein at least one of the plurality of sensors provides a signal representative of a sensed patient temperature, wherein: the microprocessor is configured to control the diverter unit to periodically redirect the fluid pathway to bypass the heat transfer catheter and interrupt fluid circulation within the heat transfer catheter and the microprocessor is configured to respond to the signals received from the at least one sensor while the fluid circulation is interrupted with a proportional integrated differential response to add heat to the heat exchange medium if the target temperature is above the patient temperature and remove heat from the heat exchange medium if the target temperature is below the patient temperature such that the patient's temperature approaches the target temperature at a controlled rate. a heat transfer catheter configured for insertion into a patient; a disposable heat exchange unit having a fluid pathway therewithin and incorporating an integral pump head adapted to move fluid through the fluid pathway; conduits coupled to the heat transfer catheter and heat exchange unit adapted to enable circulation of a heat exchange medium therebetween upon operation of the pump head; a diverter unit adapted to periodically redirect the fluid pathway to bypass the heat transfer catheter; a plurality of sensors (58a-b, 80) for providing signals representative of patient data; and a reusable master control unit having a heater/cooler and a pump driver, the disposable heat exchange unit being adapted to couple to the master control unit such that the pump driver engages the integral pump head and so that the fluid pathway is in thermal communication with the heater/cooler, the master control unit also having a microprocessor configured to receive the signals representative of the patient data from the plurality of sensors (58a-b, 80) and to control the heater/cooler in accordance with the signals received from the plurality of sensors, the microprocessor further configured to receive a target temperature input and wherein at least one of the plurality of sensors provides a signal representative of a sensed patient temperature, wherein: the microprocessor is configured to control the diverter unit to periodically redirect the fluid pathway to bypass the heat transfer catheter and interrupt fluid circulation within the heat transfer catheter and the microprocessor is configured to respond to the signals received from the at least one sensor while the fluid circulation is interrupted with a proportional integrated differential response to add heat to the heat exchange medium if the target temperature is above the patient temperature and remove heat from the heat exchange medium if the target temperature is below the patient temperature such that the patient's temperature approaches the target temperature at a controlled rate.