Disclosed are procedures and kits for nucleic acid-based molecular diagnostic determination of bacterial germ counts during which procedure evolutionarily conserved genes and genes coding for characteristic pathogenicity markers, favourably microbial enzyme, toxin, special resistance, are detected using real-time PCR amplification method with the application of fluorescent hydrolysis probes. The multiplication of nucleotide chains takes place with oligonucleotides annealing to the structural gene 5′ end region and to the adjacent upstream regulatory promoter-operator region so that the presence of the structural gene is shown along with the adjacent upstream regulatory promoter-operator sequences; the functional nature of the structural gene is simultaneously checked. The result is measured with a genome unit equivalent DNA amount calibrated to the germ number of sample units equivalent to standard procedures. The calibrated determination of bacterial germ counts is favourably based on single copy gene sequences in the genome, like those coding for characteristic pathogenicity markers.