Quantitative data comparing iron and cobalt based catalysts for the Fischer-Tropsch synthesis (FTS) are scarce due to the fact that these two kinds of catalysts typically utilize different process conditions. This paper focuses on studying the catalytic behavior of two highly active iron and cobalt based research catalysts at clean conditions and during poisoning with common syngas contaminants. The catalyst activity and selectivity at identical conditions, the CO conversion effect, and the effect of poisons on iron and cobalt catalysts were systematically explored in a quantitative manner. At a set of identical FTS conditions, the cobalt catalyst was 2.5 times as active as the iron catalyst with higher CH4 and C-5+ selectivities but much less olefins and lower CO2 selectivity. Cobalt based catalysts are more susceptible to deactivation by oxidation at high CO conversions (e.g. > 80%) due to the high partial pressure of water (P-H2O) in the reactor, while the iron catalyst can be stabilized at a high conversion level. Under clean FTS conditions, the cobalt catalysts displayed a more pronounced CO conversion effect on stability and selectivity; on the other hand, a combination of effects (i.e. from CO conversion and the nature of the catalyst) were observed for the iron catalysts. The sensitivities of the Fe and Co catalysts to the typical contaminants (i.e., H2S and NH3) present in the syngas derived from coal, natural gas or biomass were compared. Iron and cobalt catalysts exhibited similar resistance to the H2S poison (i.e. threshold levels 25-50 ppb), but the iron catalyst was found to be much more resistant to ammonia than the cobalt catalyst (i.e., threshold levels of 80 ppm and 45 ppb, respectively). Co-feeding 150-200 ppm ammonia lowered CH4 selectivity and 2-olefin content (suppressing secondary reactions of 1-olefin) on both types of catalysts. In contrast, co-feeding up to 1 ppm H2S significantly increased CH4 formation only on cobalt catalysts but had a minor effect on CH4 selectivity with iron catalysts. It increased 2-olefin content (enhanced secondary reactions of 1-olefin) regardless of catalyst type. H2S and NH3 have different impacts on H-2, CO adsorption, and the formation of sulfur and nitride compounds have been proposed to explain these dissimilar effects.