Under the influence of the change in the overall economic environment, the problem of measuring the performance of a company and its financial health is also changing. At present, every agricultural company is exposed to a number of internal as well as external risks, the failure of which can lead to potential bankruptcy. It is a known fact that the risks in agriculture are significantly greater than those in other sectors of the national economy. Proper diagnosis of critical aspects and measuring the development of individual financial indicators of agricultural holdings are basic prerequisites for eliminating these risks and maintaining, as well as increasing, their competitiveness. Among the key tools for measuring the financial situation of a company are bankruptcy models, three of which have been used (Altman model, Taffler model, and Bonity index). The aim of this study was to identify the comprehensive financial health of 469 agricultural enterprises in the Slovak Republic using the three above-mentioned bankruptcy models in 2016. The obtained results were verified using the Kruskal–Wallis test, Levene test, or Moran index. Altman's model indicated potential future problems of businesses and agricultural cooperatives. Using the Bonity index, the neutral situation was assessed (the financial health could be regarded as neither insufficient nor optimal). Taffler model offered contradicted results and does not expect the occurrence of problems soon. In the study, we also verified the assumption of the dependence of financial health of companies on the legal form and territorial division, which was confirmed to be insignificant.