The report summarises the monitoring data collected in 2016 on the presence of residues of veterinary medicinal products and certain substances in live animals and animal products in the European Union. A total of 710,839 samples were reported to the European Commission by 27 out of the 28 Member States. They consisted of 369,262 targeted samples and 21,350 suspect samples reported under Council Directive 96/23/EC, and of 4,075 samples collected at import and 316,152 samples collected in the framework of programmes developed under the national legislation. The majority of Member States fulfilled the minimum requirements for sampling frequency, laid down in Council Directive 96/23/EC and in Commission Decision 97/747/EC. Overall in 2016, the percentage of non-compliant targeted samples (0.31%) was comparable to the previous 9 years (0.25%–0.37%). In 2016, high frequencies of non-compliant samples were reported again for chemical elements (mainly metals). Over the 10 year period, the highest and lowest frequencies of non-compliant samples for non-steroidal anti-inflammatory drugs and antibacterials, respectively, were reported in 2016. Decreases in the percentage of non-compliant samples, compared to more recent years, were noted for antithyroid agents, resorcylic acid lactones and mycotoxins. This analysis should be regarded as having a certain degree of uncertainty, as it is based on partially aggregated data and the sampling plans and the spectrum of substances analysed are not necessarily the same every year.