Influenza is a contagious respiratory disease caused by viruses belonging to the family Ortomyxoviridae. Among the influenza viruses type A, B and C, the A type virus shows the most pathogenic potential. Its surface receptor glycoproteins, hemagglutinin (HA) and neuraminidase (NA), are characterized by high antigenic variation, thus a host organism cannot develop permanent resistance. The case is described of a male patient with severe acute respiratory distress syndrome in the course of influenza A/N1H1v infection, confirmed by virological molecular analysis. During diagnostic procedures based on the MSSCP genotyping it was observed that the WHO recommended RT-PCR kits and/or procedure of sample collection from patients for molecular investigation could lead to false positive A/H1N1 pandemic strain detection because of the co-amplification during the RT-PCR fragments of the human genome.