Small family-owned companies are the most common type of European business structure and are characterised by their orientation to long-term goals. Therefore, they can play an important role in the launching of businesses related to sustainable growth. However, access to finance is difficult for start-ups. Mutual Guarantee Institutions (MGIs) mitigate this problem by facilitating long-term guaranteed loans, but they must assume responsibility for default losses. This paper analyses, as of the end of 2018, the loan default of the portfolio of guarantees formalised by Spanish MGIs with new companies between 2003 and 2012, a period including both economic growth and recession. The objective is to identify the annual evolution and the average global cost of default, as well as the differences in said portfolios according to the purpose of the loan, company size and economic activity. The analysis was developed while considering two scenarios: one determinist, using a ratio method and another stochastic, using an analysis of variance. We found differences in the distribution of defaults for the variables company size and sector of activity. The findings provide relevant information for managers and Public Administrations to improve the distribution of guarantees between Spanish MGIs and public institutions, and their coverage of Small and Medium Enterprise (SME) loan defaults.