A rapid thermal processing (RTP) system including a transmission pyrometer monitoring the temperature dependent absorption of the silicon wafer for radiation from the RTP lamps at a reduced power level. A look-up table is created relating unnormalized values of photodetector photocurrents with wafer and radiant lamp temperatures. A calibrating step measures the photocurrent with known wafer and lamp temperatures and all photocurrents measured thereafter are accordingly normalized. The transmission pyrometer may be used for closed loop control for thermal treatments below 500.degree. C. or used in the pre-heating phase for a higher temperature process including radiation pyrometry in closed loop control. The pre-heating temperature ramp rate may be controlled by measuring the initial ramp rate and readjusting the lamp power accordingly. Radiation and transmission pyrometers may be included in an integrated structure with a beam splitter dividing radiation from the wafer.