Endurance running is well-documented to affect health beneficially. However, data are still conflicting in terms of which race distance is associated with the maximum health effects to be obtained. Therefore, the aim of this study was to compare the health status of endurance runners over different race distances. A total of 245 recreational runners (141 females, 104 males) completed an online survey. Health status was assessed by measuring eight dimensions in two clusters of health-related indicators (e.g., body weight, mental health, chronic diseases and hypersensitivity reactions, medication intake) and health-related behaviors (e.g., smoking habits, supplement intake, food choice, healthcare utilization). Each dimension consisted of analytical parameters derived to a general domain score between 0 and 1. Data analysis was performed by using non-parametric ANOVA and MANOVA. There were 89 half-marathon (HM), 65 marathon/ultra-marathon (M/UM), and 91 10-km runners. 10-km runners were leaner than both the HM and M/UM runners (p ≤ 0.05). HM runners had higher health scores for six dimensions (body weight, mental health, chronic diseases and hypersensitivity reactions, medication intake, smoking habits, and health care utilization), which contributed to an average score of 77.1% (score range 62–88%) for their overall state of health. Whereas 10-km and M/UM runners had lesser but similar average scores in the overall state of health (71.7% and 72%, respectively). Race distance had a significant association with the dimension “chronic diseases and hypersensitivity reactions” (p ≤ 0.05). Despite the null significant associations between race distance and seven (out of eight) multi-item health dimensions, a tendency towards better health status (assessed by domain scores of health) among HM runners was found compared to other distance runners. However, the optimal state of health across all race distances supported the notion that endurance running contributed to overall health and well-being.Trial registration number: ISRCTN73074080. Retrospectively registered 12th June 2015.