In vitro glucuronidation assays of diclofenac and indomethacin at pH 7.4 are biased by the instability of the glucuronides due to acyl migration. The extent of this acyl migration may be reduced significantly by performing the glucuronidation reaction at pH 6.0. Testing the human UDP-glucuronosyltransferases (UGTs) of subfamilies 1A, 2A and 2B at pH 7.4 revealed that UGT1A10, UGT2B7 and UGT2B17 are the most active enzymes in diclofenac glucuronidation, while the highest indomethacin glucuronidation rates (corrected for relative expression levels) were exhibited by UGT2A1, UGT1A10 and UGT2B7. Interestingly, lowering the reaction pH to 6.0 increased the activity of many UGTs, particularly UGT1A10, toward both drugs, even if the rate of 4-methylumbelliferone glucuronidation by UGT1A10 at pH 6.0 was significantly lower than at pH 7.4. On the other hand, UGT2B15 lost activity upon lowering the reaction pH to 6.0. UGT1A6 does not glucuronidate diclofenac and indomethacin. Nevertheless, both drugs inhibit the 1-naphthol glucuronidation activity of UGT1A6 and their inhibition was stimulated by lowering the reaction pH, yielding significantly lower IC(50) values at pH 6.0 than at pH 7.4. In conclusion, glucuronidation reactions pH affects their outcome in variable ways and could increase the toxicity of drugs that carry a carboxylic acid.