Sample geometry has been shown to be a significant factor in determining the actual temperature of samples annealed in thermocouple controlled rapid thermal processing systems. Temperature differences of nearly 25 °C have been observed between full 4 in. wafers and quarter wafers under identical annealing conditions. Some of the geometry effects observed can affect the validity of temperature measurements in pyrometer controlled systems as well. The changes in sample temperature can be measured directly via thermocouples, and indirectly via secondary ion mass spectrometry (SIMS) and resistivity mesurements of ion implanted samples. Smaller samples are observed to heat up faster, and obtain a slightly higher maximum temperature than larger samples. Based on computer modeling this effect is attributed to the absorption of reflected/scattered radiation in addition to that directly incident on the sample. Small samples placed on top of full wafers during annealing are observed to heat up more slowly than the underlying wafer. This effect is likely due to imperfect thermal contact between the samples during the anneal. Small boron implanted samples annealed on top of whole wafers such that the implanted side is in contact with the whole wafer appear to experience a slight reduction in boron outdiffusion, similar to the reduced As outdiffusion observed for comparable anneals of GaAs wafers. In order to correctly compare reported temperature data from the literature, these geometry effects must be taken into consideration.