Isothiocyanates have been implicated in the cancer-protective effects of brassica vegetables. When cabbage is consumed, sinigrin is hydrolysed by plant or microbial myrosinase partly to allyl isothiocyanate (AITC), which is mainly excreted as N-acetylcysteine conjugates (NAC) of AITC in urine. The effect of cooking cabbage on the excretion of NAC of AITC, and glutathione-S-transferase (GST) and uridine 5′-diphospho-glucuronosyl transferase (UGT) activity in rat liver and colon was investigated. Germ-free (GF) and human faecal microbiota-associated (HFM) rats were fed a control diet containing 20 % raw, lightly cooked, or fully cooked cabbage for 14 d. When plant myrosinase was present, excretion of NAC of AITC/24 h was increased by 1·4 and 2·5 times by the additional presence of microbial myrosinase after consumption of raw and lightly cooked cabbage respectively. When plant myrosinase was absent, as after consumption of fully cooked cabbage, excretion of the AITC conjugate was almost zero in GF and HFM rats. None of the cabbage diets modified hepatic GST activity. When microbiota was absent, colonic GST was 1·3-fold higher after fully cooked cabbage, and hepatic UGT was increased by 1·4–1·8-fold after all cabbage diets, compared with the control feed. There were no differences in GST or UGT following cabbage consumption when microbiota was present. It is possible that other constituents of cabbage, rather than metabolites of glucosinolates per se, may be responsible for changes in phase 2 enzyme activity. The main effect of cooking cabbage and altering colonic microbiota was on excretion of NAC of AITC.