Chambers are the most common method used to sample soil-atmosphere fluxes of trace gases. Working in tree plantations in Costa Rica and in subtropical forest in Puerto Rico, we performed controlled experiments in order to evaluate whether installation of the chamber bases into the soil affects the soil-atmosphere flux of nitrogen oxides. Installation of chambers servered roots. We found a short-term disturbance effect related to chamber installation. Fluxes of nitrogen oxides increased by as much as a factor of 4 during a period of about 1 month following chamber installation in the soil. Within 6 weeks of chamber base installation, fluxes fell to control levels. Given the timescale of disturbance and recovery, root mortality and decomposition is the most likely cause of the observed effect.