Antibiotics and chemotherapeutics are sometimes used in beekeeping, resulting in residues in honey. In the EU, no Maximum Residue Limits (MRLs, Commission Regulation (EU) No 37/2010 and amendments) have been established so far for anti-infectious agents in honey. For a long period, a zero-tolerance for any presence of residues of antibiotics in honey was respected, but actually a judgement based on scientific risk assessment should be applied. Many microbiological, immunological and receptor tests have been developed for screening for residues of anti-infectious agents in honey, besides chromatographic methods for screening or confirmation. Some active compounds are very stable in honey while other compounds metabolize or degrade. Hence, for residue analysis it is important to look for the suitable marker residues. In some cases the presence of antimicrobial residues in honey is not related to apicultural use. The results of monitoring studies regarding the occurrence of antimicrobial residues in honey on the Belgian and European market are discussed.