Near infrared spectroscopy is an increasingly important tool for the investigation of human brain function, however, to date there have been few systematic evaluations of accompanying thermal effects due to absorption. We have measured the spatial distribution of temperature changes during near infrared irradiation (789 nm) as a function of laser power, in both excised tissue (chicken meat and skin) and in the forearm of an awake human volunteer. Light was applied using a 1 mm optical fiber which is characteristic of the topographic system. The temperature of excised chicken tissue increased linearly with power level as 0.097 and 0.042°C/mW at depths of 0 and 1 mm, respectively. Human forearm studies yielded temperature changes of 0.101, 0.038, and 0.030°C/mW at depths of 0.5, 1.0, and 1.5 mm, respectively. Due to direct irradiation of the thermocouple all measurements represent the maximum temperature increase from the laser. In all cases the estimated heating effects from continuous wave optical topography systems were small and well below levels which would endanger tissue cells. The close similarity between ex vivo and in vivo measurements suggests negligible contributions from blood flow in the skin which was further supported by measurements during cuff ischemia. Heating effects decreased sharply with both depth and lateral position; thus, for optode spacings greater than a few millimeters, fibers can be treated independently. Finite element analysis confirms that the experimental results are consistent with a simple heat conduction model.