Incubation trials were carried out with the rumen simulation technique (RUSITEC) to study the effects of bag pore size (40, 100 and 200 μm) and dilution rate (2.3%/h and 3.5%/h) on the fermentation parameters and number of protozoa when a high forage diet was incubated. The lower dilution rate resulted in a decrease in pH and an increase in the molar proportion of butyrate, but the disappearance of the diet from the bags was not affected. Protozoal counts were not affected by dilution rate, but holotrichs disappeared completely at low dilution rate as a consequence of low pH. Disappearance of the diet from the bags was higher with 100 μm than with 40 μm bags, but this could not be explained by higher washing losses. Numbers of protozoa were lower with 40 μm than with 100 μm bags, and large protozoa were not present when 40 μm bags were used. There was no difference in protozoa counts between pore sizes of 100 μm and 200 μm and large protozoa were present with both of them. However, disappearance of the diet from the bags and methane and acetate productions were higher ( P < 0.05) with 100 μm bags than with those of 200 μm. Our results indicate that pore size of the bags in RUSITEC affects not only the disappearance of the diet, but also the microbial population in the system and therefore the fermentation.