The pool size of bacterial and protozoal matter in rumen fluid and the microbial matter passage rate to the omasum were determined in 3 sheep fed 750 g hay and 130 g ground barley every 12 h. The animals were either ciliate free or selectively faunated with Eudiplodinium maggii, Diploplastron affine, Entodinium caudatum, or natural protozoal fauna. Murein β-glycans were used as a marker to quantify the bacterial matter, whereas the dry matter content of single ciliates and their number were used to calculate protozoal matter. It was found that the total bacterial matter in the rumen fluid of ciliate-free sheep was 216 g and the pool size arriving in the duodenum, 231 g dry matter (DM). The protozoal matter varied from 24 to 71 g DM in the rumen fluid and from about 18 to 71 g DM in omasal influent. The dry matter of ciliate-associated bacteria varied from 11 to 23 g in the rumen and from over 5 to 23 g in the omasal influent. The establishment of ciliates reduced the pool size of bacterial matter by 17%-39% in the rumen and by 20%-38% in the omasal influent.