The bacterial β-glucuronidase (GUS) gene is often introduced into plants as a reporter gene fused to a promoter because of advantages over other reporter genes. However, many plants have non-neglegible levels of endogenous GUS or GUS-like activity which can interfere with the activity originating from the introduced GUS gene, especially if this level is a low one. To eliminate the endogenous GUS activity, we studied the effect of some water-soluble organic solvents on decreasing it and found that addition of methanol at 20% volume to a GUS reaction mixture was very effective, lowering the endogenous activity to 0–15% of the origin in all plant extracts tested. Moreover, methanol at this concentration enhanced by 1.4-fold the activity originating from the introduced GUS gene or GUS purified from E. coli. This method enabled us to determine GUS gene expression more reliably, after introduction of GUS gene fusion into rice protoplasts. In histochemical GUS analysis of transgenic tobacco, this method was also effective for suppressing the endogenous GUS activity.