The in vitro ammonia production and ruminal in situ disappearance of dry matter, organic matter, protein and ether extract of heat-treated whole cottonseed were determined. Abomasal flow of nitrogen and ether extract and terminal ileal flow of lysine and methionine of heat-treated whole cottonseed were also evaluated. Whole cottonseed was treated with microwaves at 85, 115, 130, 144 and 155 Â°C for 5, 10, 15, 20 and 30 min. Heat treatment at 144 Â°C and 155 Â°C reduced in vitro ammonia production for all treatment durations. The effective ruminal disappearance of dry matter, organic matter, protein and ether extract was also decreased by heat treatment. Protein degradation was decreased from 54.2% to 29.5% at a fractional rumen outflow rate of 0.08/h while ruminal in situ ether extract disapÂ¬pearance was decreased from 47.8% to 28% with heat treatment at 155 `C. for 20 min. Abomasal flow of nitrogen increased by 15% with heat treatment. Lysine and methionine flow in the terminal ileum was not influenced by heat treatment. Whole cottonseed treated at 155 Â°C for 20 min apparently gave the best protection for protein against rumen degradation and for increasing the proportion of rumen inert fat.