A study was performed to examine differences in hip and thigh muscle activation in male and female runners with and without iliotibial band syndrome (ITBS). The muscle activation of 21 runners (14 with ITBS and 7 healthy) was recorded during a run. No significant differences were observed in mean muscle activation between injured male and female runners. In contrast, in female runners with ITBS, there were differences in activation between the vastus lateralis and the tensor fascia lata (p<0.05), and between the vastus lateralis and the biceps femoris (p<0.05). With regard to male runners with ITBS, differences in activation were observed between the gluteus maximus and the tensor fascia lata, and between the gluteus maximus and the biceps femoris (p<0.05). These findings contribute to a better understanding of iliotibial band syndrome and may be useful for designing of targeted treatments for the ITBS.