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Automated analytical instruments for enumerating indicator organisms and diagnostic test kits for pathogens can be used in food microbiology to screen samples and to replace conventional cultural and confirmation steps. Such methods are now available for rapid detection or estimation of groups of (indicator) organisms, pathogenic micro-organisms, bacterial toxins and mycotoxins, and molds. These alternative methods can be classified by the principles on which they are based: modified conventional methods, instrumental measurement of bacterial metabolism, bioluminescence, immunological techniques, DNA techniques, and combinations of these techniques. To meet user expectations, test kits must be accurate, sensitive, specific, rapid (24 h or less), easy to use, and labor-saving. They must also offer the possibility of computerization, a low detection limit, and low investment and running costs. The paper compares the ability of alternative methods to meet these criteria. Variations were found, depending on the techniques used and the target organism of the analysis. Economic reasons can determine whether alternative methods can be used routinely. Adoption of these screening systems also can be hampered by lack of internationally coordinated and accepted validation protocols.