A multiple-loop temperature controller (50,72) using RTD sensors (82) is continuously calibrated by performing a zero or full scale calibration during each operating cycle. An arrangement of four multiplexers (74-80) is used to successively connect each RTD sensor (82) to a pair of current sources (84,86) and an A/D converter (92), thereby allowing the current sources (84,86) and A/D converter (92) to be shared among all of the RTD sensors (82). Measurement errors are minimized by using the same multiplexers (74-80) for temperature measurement and calibration, with calibration being performed by connecting the multiplexers (74-80) to a ground reference or precision resistor (112). Interrupt-driven temperature loop processing is used to reduce A/D conversion delays, thereby allowing high-precision A/D converters with long settling times to be used. The multiple-loop temperature controller (50,72) is advantageously utilized in an automated blood culturing system (10) requiring precise control of sample temperatures.