Intense competition in past decades, stemming from the opening of national markets and global expansion of production, has forced companies to use all their best resources and core skills to exploit business opportunities.Companies compete in a fast-changing environment, where the key question is how to succeed in such an environment. The only viable answer is to act in such a way to achieve and sustain a competitive advantage through continuous innovation. Companies' performance at different levels of innovation also reflects their innovation performance at the national level. This paper's driving research question examines the innovation performance of companies and, based on the results, defines the main challenges of selected countries to improve companies' innovation abilities and performance. Several methodologies to measure innovation abilities and performance of companies exist; this paper is based on two of them. The first one is the European Innovation Scoreboard, which assesses the innovation performance of selected countries using the Community innovation Survey database. The second is based on SME Performance Review Indicators, which measure the performance of European SMEs in different areas, including innovativeness. These two sources represent the database for the empirical comparison of Slovenia and Croatia. The results indicate that several differences exist between the compared countries and that both face many challenges in developing innovation capabilities of companies and improve policies and mechanisms supporting innovativeness to improve companies' innovation performance.