My 6 years old daughter is complaining that her knees are aching when she is running?

Knee pain: knee pain in young children can have many sources. If it persists especially if there is swelling or tenderness you should have it evaluated by her pediatrician.

See a physician: Don't know enough detail.Pain without swelling as well as symmetry suggests benign process.I see children with knee pain and most commonly there is a pattellofemoral malalignment,hyper flexibility plays a role.

See pediatrician: This symptom should not be ignored. It may signify an arthritic condition or a problem with the circulation and stability of the growth plates of the bones of the knee . A pediatrician should be consulted soon.