During 54 days in Summer 2000 CO₂ and energy fluxes were measured with an open-path (OP, Licor Li7500) and a closed-path (CP, Licor Li6262) based eddy covariance system at a young ponderosa pine site. Good agreement between measured half-hour CO₂ fluxes by the open-path (F_c.op) and the closed-path (F_c.cp) based system were found (F_c.cp=1.033 * F_c.op + 0.706 µmol m^-2 s^-1, n=2475, r²=0.95) , but consistent small differences are evident at night, with the CP system estimating ~1.0 µmol m^-2 s^-1 higher respiration on average. Daytime differences between the OP and CP systems were smaller, with the CP system estimating ~0.4 µmol m^-2 s^-1 lower F_c during the daytime. Overall differences between OP and CP systems appeared to be systematic and lead to a significant different estimate of cumulative net ecosystem exchange (NEE). Cumulative NEE over the 54 days was a net uptake of -33 gC m^-2 for the CP system and -72 gC m^-2 for the OP system, i.e. the CP estimate was 54% smaller than the OP estimate. Additional comparison above other ecosystem (Winter wheat after harvest, old-growth deciduous forest) seem to indicate a similar pattern. This presentation will discuss influences of co-spectral decomposition, density flux term (Webb et al, 1980), and corrections for frequency response loss.