Background: Since knee complaints are common among athletes and are frequently presented in general practice, it is of interest to investigate the type of knee complaints represented in general practice of athletes in comparison with those of non-athletes. Therefore, the aim of this study is to investigate the differences in type of knee complaints between sport participants, in this study defined as athletes, and non-sport participants, defined as non-athletes, presenting in general practice. Further, differences in the initial policy of the GP, medical consumption, and outcome at one-year follow-up were also investigated. Methods: Patients consulting their GP for a new episode of knee complaints were invited to participate in this prospective cohort study. From the total HONEUR knee cohort population (n = 1068) we extracted patients who were athletes (n = 421) or non-athletes (n = 388). Results: The results showed that acute distortions of the knee were significantly more diagnosed in athletes than in non-athletes (p = 0.04). Further, more athletes were advised by their GP to 'go easy on the knee' than the non-athletes (p < 0.01), but no differences were found in number of referrals and medication prescribed by the GP. The medical consumption was significantly higher among athletes; however, no significant differences were found between the two groups for recovery at one-year follow-up. Conclusion: There are no major differences in the diagnosis and prognosis of knee complaints between athletes and non-athletes presented to the GP. This implies that there are no indications for different treatment strategies applied in both groups. However, athletes are more often advised to 'go easy on the knee' and to rest than non-athletes. Further, there is a trend towards increased medical consumption among athletes while functional disability and pain are lower than among the non-athletes.