Each of the four accredited laboratories is, apart from other things, specialised for some kinds of analyses.

The laboratory of the Prague inspectorate is specialised for the determination of vitamins, pesticides, for methods of testing spirit and others. The laboratory in Brno specialises, e.g., for the methods of wine testing and detection of GMO in food. The laboratory in Hradec Králové is mainly specialised for the determinations of chemical agents, organochlorine pesticides, polychlorinated biphenyls, and the laboratory in Olomouc performs mainly analyses of mycotoxins, aflatoxins first of all. The laboratories of inspectorates in Tábor, Plzeň and Ústí nad Labem perform only microbiological analyses of food.

Since 1993, CAFIA has been organising on regular basis the inter-laboratory comparison tests within the ILPT system (inter-laboratory proficiency testing) that have been included in the National comparison testing system. The organisation and assessment of the ILPT system are held in cooperation with CAI (Czech Accreditation Institute). In 2001 the following rounds of the comparison tests were held or initiated:

• § Determination of sorbic acid and sulphur dioxide in wine
• § Determination of the contents of alcohol, sugar, sugar-free extract and volatile acids in wine
• § Determination of vitamins in food for special dietary uses
• § Determination of phthalates, benzene, toluene, xylene, ethylcarbamates, methanol and higher alcohols in liquor
• § Determination of nitrates in meat-vegetable products
• § Determination of cyclamate in beverages
• § Determination of acidity coefficient, pH, refractometric dry matter in beverages
• § Determination of the selected microorganisms in food

The CAFIA laboratories regularly take part in the international comparison tests. In 2001 CAFIA participated in the tests within the FAPAS system (physical and chemical determinations) and FEPAS system (microbiological determinations) held in Britain, in the tests within the CHEK system (physical and chemical determinations) held in the Netherlands, and in the tests carried out in the area of microbiology that were held in Sweden, and others.