The present study analyzed the impact of the running style and the morphologic and functional characteristics of the foot on the incidence of non-traumatic foot and lower limb disorders in runners. From January 2004 to December 2008, we prospectively examined 166 runners, both recreational and competitive, involved in various running specialities, from three athletics clubs in Northern Italy. They were 86 males and 80 females, with a mean age of 31.1 ± 12.2 years. We considered non-traumatic foot and lower limb diseases reported during the follow-up period, which resulted in a minimum sport rest of two weeks. The incidence of these diseases was examined with respect to general characteristics, type of activity, foot morphology, running style. 59% of athletes reported one or more diseases. The most common were plantar fasciitis (31% of athletes) and Achilles tendinopathies (24%). Overall, the more prone to injuries were males (60.9% of cases), competitive runners (70.9%), middle-distance runners (51.7%), and those using spike shoes (80.3%). Age, body weight and height were not important predictors of running injuries in general. Considering the morphological characteristics of the foot, the most prone to injury were the varus hindfoot (87.5% of cases) and the cavus arch (71.4%). In conclusion, a deep knowledge of the factors predisposing runners to specific diseases, often chronic and highly debilitating for the athlete, may allow implementing effective therapeutic measures.