The carbon isotope method (AOAC 998.12) compares the bulk honey carbon isotope value with that of the extracted protein; a difference greater than 1‰ suggesting that the protein and the bulk carbohydrate have different origins. New Zealand Manuka honey is a high value product and often fails this test. It has been suggested such failures are due to the pollen in the Manuka honey and an adaptation of the method to remove pollen prior to testing has been proposed. Here we test 64 authentic honey samples collected directly from the hives and find that a large proportion (37%) of Manuka honeys fail the test. Of these 60% still fail the adapted method. These honey samples were collected and processed under stringent conditions and have not been adulterated post-harvest. More work is required to ascertain the cause of these test failures.