In the work there is an innovative methodology of problem analysis presented in the quality management system with the use of systems approach. The methodology serves for determination of action mechanism of unfavorable phenomena occurring in the systems and for explaining their causes. There are assumptions of the elaborated methodology described. For the first time there are the rules of systems thinking used for the analysis of unfavorable phenomena and the system archetypes were applied. Special attention is paid to appropriate presentation of the examined situation in a perspective of systems thinking as well as correct selection of systems archetype. There is a need emphasized concerning examining the situation with the inclusion of numerous variables and necessity to reach to the primary causes of the analyzed phenomena. The elaborated methodology was proceeded to validation on the basis of two threats described by different systems archetypes. There are schemes presented which feature the action mechanism of unfavorable phenomena. The confirmation of methodology in practice proved its application possibilities. Finally, the elaborated methodology was subject to analysis. The discussion of its possibilities and limitation was also conducted.
 M. Jackson. Systems methodology for the management sciences. Plenum Press, New York, 1990.
 M.C. Jackson. Systems thinking: Holism for managers. Wiley, Chichester, 2003.
 R. Floor and M. Jackson. Creative problem solving: Total systems intervention. Wiley, Chichester, 1991.
 J.P. Kawalek. “Systems thinking and knowledge management: positional assertions and preliminary observations”, Systems Research and Behavioral Science, no 21, 2004, pp. 17-36.
 M.J. Ligarski. „Ocena systemu zarządzania jakością – wyniki badań”, Towaroznawcze Problemy Jakości, nr 4 (13), 2007, pp. 25-35.
 M.J. Ligarski. Podejście systemowe do zarządzania jakością w organizacji. Monografia, Wyd. Politechniki Śląskiej, Gliwice, 2010.
 M.J. Ligarski. “Problem identification method in certified quality management systems”, Quality & Quantity, vol. 46, 2012, pp. 315-321.
 M.J. Ligarski. “Problems examination in quality management system”, Acta technologica agriculturae vol. 16, no. 4, 2013, pp. 106-110.
 M.J. Ligarski. „Diagnoza systemu zarządzania w polskich organizacjach”, Problemy Jakości, nr 5, 2014, pp. 14-22.
 Paucar-Caceres. “Operational research, systems thinking and the development of management sciences methodologies in the US and the UK”, Scientific Inquiry: A Journal of the International Institute for General System Studies, vol. 9, no. 1, 2008, pp. 3-18.
 Paucar-Caceres and R. Pagano. “System thinking and the use of systemic methodologies in knowledge management”, Systems Research and Behavioral Science, no. 26, 2009, pp. 343-355.
 L.L.R. Rodrigues, N. Dharmaraj, B.R. Shrinivasa Rao. “System dynamics approach for change management in new product development”, Management Research News, vol. 29, no. 8, 2006, pp. 512-523.
 P.M. Senge. The fifth discipline The art and practice of the learning organization. Doubleday/Currency, New York, 1990.
 P.M. Senge. Piąta dyscyplina Teoria i praktyka organizacji uczących się. Oficyna Ekonomiczna, Polskie Wydawnictwa Profesjonalne sp. z o.o., Wolters Kluwer Polska sp. z o.o., Warszawa, 2006.
 P.M. Senge, A. Kleiner, C. Roberts, R.B. Ross, B.J. Smith. The fifth discipline Fieldbook Strategies and tools for building a learning organization. Doubleday, London 1994.
 P.M. Senge, A. Kleiner, C. Roberts, R.B. Ross, B.J. Smith. Piąta dyscyplina materiały dla praktyka Jak budować organizację uczącą się. Oficyna Ekonomiczna, Polskie Wydawnictwa Profesjonalne sp. z o.o., Kraków, 2002.
 E. Wolstenholme. “Towards the definition and use of a core set of archetypal structures in system dynamic”, System Dynamics Review, vol. 19, no. 1, 2003, pp. 7-26.
 E. Wolstenholme. “Using generic system archetypes to support thinking and modeling”, System Dynamics Review, vol. 20, no. 4, 2004, pp. 341-356.