Introduction: Football and handball are complex contact sports with a relatively high risk of musculoskeletal injuries in athletes. Football and handball, with their characteristics in which high-intensity movements stand out and exceptional motor skills, also require periods of rest necessary for adequate muscle tissue recovery. Knowing the specifics of musculoskeletal injuries in football and handball players will result in more precise guidelines for creating preventive programs. Aim: This research aimed to examine whether there is a difference in the incidence of musculoskeletal injuries between football and handball players. The specific goals of this research were to determine whether the incidence of musculoskeletal injuries of the lower and upper extremities is higher in football or handball players, the relationship between the incidence of injuries, the length of experience in professional sports and the length of the rest period between training sessions. Participants and methods: 166 examinees from the entire Croatian republic participated in this research. The examinees were senior football and handball players who play in the First, Second, Third or Fourth Croatian Football or Handball Leagues. To collect the data needed for this research, an online questionnaire designed for the needs of this research was used. Data and results were processed using the Statistica and Microsoft Excel programs. The analysis of the sampled data was done using descriptive and comparative statistics. Results: The collected data generally determined no incidence difference in musculoskeletal injuries between football and handball players. Considering the specificity of localization, injuries of the lower extremities are more frequent among football players than handball players, while injuries of the upper extremities are more frequent among handball than football players. Injuries are higher in athletes with more extended experience in professional sports. The resting period between training sessions is not related to the incidence of athlete injuries. Conclusion: Based on the results of this research, we can conclude that there is no difference in the incidence of injuries between football and handball players. This research aims to raise awareness of the importance of continuous education of professional staff on the specificity of the injuries of football and handball players, which would improve the available preventive programs to reduce athletes injuries and improve their performance.