The European Patent Convention contains a prohibition on the grant of patents for "methods of treatment of the human or animal body by surgery or therapy and diagnostic methods practiced on the human or animal body." A 1987 Appeal Board decision, Non-invasive measurement/Bruker, held that the only diagnostic methods that are excluded from patent protection are those whose results immediately make it possible to decide a particular course of medical treatment. As a result of this, it had been held that methods which produce only interim results are not barred from patentability.

The issue which arose in the case of Device and method for sampling substances using alternating polarity/Cygnus Inc. was whether these provisions prevented the grant of a European patent for a method which involved obtaining a sample from a surface tissue of a human or animal body by extracting the substance of interest through the surface tissue by application of an electric current in a first polarity, analyzing the sample obtained for the concentration of a particular chemical and then repeating the operation using an electric current of reversed polarity.

The Appeal Board hearing the case started by noting that the decision in Non-invasive measurement/Bruker was not fully consistent with decisions applying the prohibitions on patents for surgical and therapeutic treatments where case law had barred the grant of patents, even if the step claimed was only an intermediate one. From this, after considering the French language text of the convention, which it found to be inconsistent with the Non-invasive measurement decision, the Board went on to conclude that the prohibition on patentability in the European Patent Convention applied to "all methods practised on the human or animal body which relate to diagnosis or which are of value for the purposes of diagnosis," irrespective of whether a physician could immediately decide on a course of treatment on the basis of the results obtained.