AbstractMethods for the determination of 2–6‐diaminopimelic acid (DAPA) and 2‐aminoethylphosphonic acid (AEP) are described. The DAPA method consists of hydrolysing the sample, its purification on charcoal columns, separation of DAPA from proline on columns of an anionic resin, and the determination of DAPA with acid ninhydrin. The AEP method consists of hydrolysing the sample with hydrochloric acid, separation of AEP from inorganic phosphate on columns of a cationic resin, hydrolysis of the P‐C bond in AEP with perchloric acid and the determination of AEP as phosphate. Examples of analysis of foods, gut contents and microbial fractions ar