The thermoelectric transport properties in atomic scale conductors consisting of a Si atom connected by two electrodes are investigated. It is found that both the electrical current and the heat current have two contributions, one from the voltage and the other from the temperature gradient. The quantities such as the Seebeck thermopower and the thermal conductance that characterize the thermoelectric transport properties of the tunnel atomic junction are studied quantitatively with a first-principles technique within the framework of Landauer-Buttiker formalism in the linear response regime. A finite thermopower only exists in a very narrow range where the energy derivative of the transmission function is nonzero. The thermopower anomaly is observed in the tunneling regime in this device but this does not violate the thermodynamic law with respect to the heat current. (C) 2004 American Institute of Physics.