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Personnel risk significantly affects the operation of small and medium-sized enterprises. The aim of the paper is to define and present significant factors affecting the perception of personnel risk in the SME segment, and compare the current status and development in the Czech Republic and Slovakia. The empirical research was conducted in 2020 in the SME segment in the Czech Republic and Slovakia via an online questionnaire, using a sample of 822 respondents. The obtained data were evaluated using the Chí square and Z score. Personnel risk significantly affects the SME segment and its business activities. This risk is perceived as the most significant business risk in both countries, even though its intensity is moderate and does not have a heavy negative impact on SMEs’ activities. The overall evaluation of personnel risk’s impact on SMEs’ activities is similar in both countries. The evaluation of employee turnover was relatively positive, as a considerable part of entrepreneurs stated that turnover is low and does not have a negative impact on their business. The evaluation of turnover was similar in both countries. Based on entrepreneurs’ statements, there are certain gaps in employee error rate, which affects their business. Slovak entrepreneurs provided a worse evaluation of the quality of their employees than the Czech entrepreneurs. Entrepreneurs in both countries are dissatisfied with the way their employees strive to improve their performance or how they compete among each other. The comparison based on business size and age did not yield significant differences, nor did it provide a clear trend despite the general belief presented in literature that larger enterprises have a better access to important fields of business management.