In order to demonstrate the presence or absence of a pyrroloquinoline quinone (PQQ) synthesizing capacity in microorganisms, we have found that media and equipment must be treated to remove contaminating PQQ. Procedures are described which appear to be effective for that purpose. These have been used with Acinetobacter calcoaceticus PQQ- strains to develop a sensitive and reliable assay for PQQ. They also have been used to show that under our conditions of growth Escherichia coli does not synthesize PQQ. Fluorescence spectroscopy is not selective enough to detect PQQ in a protein hydrolysate due to background fluorescence in the same spectral regions as PQQ. In addition, PQQ reacts with amino acids to give products that cannot be detected by either fluorescence spectroscopy or biological assay. In this regard, claims that several materials originating from plants or animals contain PQQ should be reexamined. Moreover, PQQ cannot be detected with these methods in hydrolysates of enzymes containing covalently bound PQQ.