Background: Generalised Joint Hypermobility (GJH) is suggested as an aetiological factor for knee injuries in adolescents and adults. It is presumed that GJH causes decreased joint stability, thereby increasing the risk of knee injuries during challenging situations like jumping and landing. The aim was to study the extent and risk of knee injuries in children with GJH and knee hypermobility. Methods: In total, 999 children (9-14 years) were tested twice during spring 2012 and 2013 with Beighton's Tests (BT) for hypermobility, a 0-9 scoring system. GJH was classified with cut-point >= 5/9 on both test rounds. On basis of weekly cell phone surveys of knee pain, children requiring clinical examination were seen. Traumatic and overuse knee injuries were registered by WHO ICD-10 diagnoses. Logistic regression and Poisson regression models with robust standard errors were used to examine the association between GJH and knee injuries, taking into account clustering on school class levels. Results: Totally, 36 children were classified GJH on both test rounds. Overuse knee injuries were the most frequent injury type (86 %), mainly apophysitis for both groups (61 %), other than patella-femoral pain syndrome for the control group (13 %). For traumatic knee injuries, distortions and contusions were most frequent in both groups (51 % resp. 36 %), besides traumatic lesions of knee tendons and muscles for the control group (5 %). No significant association was found between overuse knee injuries and GJH with/without knee hypermobility (OR 0.69, p = 0.407 resp. OR 0.75, p = 0.576) or traumatic knee injuries and GJH with/without knee hypermobility (OR 1.56, p = 0.495 resp. OR 2.22, p = 0.231). Conclusions: Apophysitis, distortions and contusions were the most frequent knee injuries. Despite the relatively large study, the number of children with GJH and knee injuries was low, with no significant increased risk for knee injuries for this group. This questions whether GJH is a clinically relevant risk factor for knee injuries in school children aged 9-14 years. A fluctuation in the individual child's status of GJH between test rounds was observed, suggesting that inter-and intra-tester reproducibility of BT as well as growth may be considered important confounders to future studies of children with GJH.