The deposit insurance system is a form of banking regulation that protects depositors and provides stability in the banking system. It is an important part of the financial safety net, especially in times of economic turmoil, as it provides explicit depositor protection and prevents a ‘bank run’. However, there are some negative effects on banking stability associated with the increase in bank risk, i.e., moral hazard, adverse selection and the principal-agent problem. The functioning of the deposit insurance system depends on its determinants, but also on the characteristics of the national banking system, supervision, legal and cultural framework and the general development of the country. Considering that the banking systems in EU and especially in comparison to Southeast European countries are very different, the aim of this paper is to study the impact of the deposit insurance system on bank stability depending on the characteristics of banks. Bank stability is analysed using bank risk variables: z-score and ratio of non-performing loans to total loans. By applying a dynamic panel analysis using the GMM Arellano–Bond (AB) estimator to a sample of EU countries and selected Southeast European countries, we provide further evidence on the deposit insurance system over the period from 2005 to 2014. The results provide evidence that large and systemically important banks behave in a riskier way, distorting the purpose of the deposit insurance scheme and jeopardising the safety of banking systems.