Aims: Enrichment of wheat bran (WB), corn meal (CM) and barley flakes (BF) with the oleaginous fungus Cunninghamella echinulata (CE) might lead to effective use of these by-products in ruminant nutrition. We examined their effects on rumen fermentation and lipid metabolism. Methods and Results: WB, CM and BF substrates without or with brewer's grains (WBG, CMG, BFG) and enriched with CE were incubated with meadow hay (MH, 500 : 500, w/w) in rumen fluid in vitro for 24 h. The dry matter of the CE-enriched substrates increased (by 2-4%); however, digestibility decreased (P < 0.01). Adverse effects of CE-enriched substrates on the rumen ciliate population were observed. Little effect on the rumen eubacterial population was detected by the 16S-polymerase chain reaction/denaturizing gradient gel electrophoresis method. The increase in gamma-linolenic acid output in the MH + BFGCE diet (800 : 200, w/w) was accompanied by an increase in rumen biohydrogenation of polyunsaturated fatty acids. Conclusion: The diet substrates enriched with the fungus CE were less digestible than the untreated cereal substrates; no appreciable positive effect was observed on rumen fermentation patterns or the eubacterial and ciliate populations. Significance and Impact of the Study: The in vitro study showed that adding CE-enriched substrates to ruminant diets is not effective for improving rumen fermentation.