A horse that pops his head up during transitions is one of the most commonly seen way-of-going problems in everyday riding, and it generates a disproportionate amount of incorrect diagnosis because the symptom — the head coming up — is so visible that riders naturally focus on the head itself rather than on what is producing the head movement. The head going up in a transition is almost never a head problem. It is a back, hindquarter, contact, or preparation problem that expresses itself most visibly at the head and neck because the horse's topline is a continuous connected system. Physical causes are the first consideration. A horse whose hind end is sore will hollow his back and raise his head at the moment of a transition because the transition demands engagement and loading of the hindquarters that produces pain. Dental issues that create asymmetrical or general bit discomfort produce head raising at the moments of rein contact change that transitions create. Saddle fit problems that produce pressure during the shifting that transitions produce create the same defensive raising response. The most common training-related cause is rein pressure applied incorrectly at the moment of the transition. Many riders ask for a downward transition by closing both hands and pulling backward — creating a fixed backward pressure against which the horse braces and raises his head to escape. The correct downward transition is ridden with leg into a softening hand — the leg maintains impulsion while the hand softens and redirects the energy rather than blocking it. Upward transitions that produce head raising are typically caused by an insufficiently following hand that does not allow the horse to reach forward into the new gait. When a horse steps into a trot from a walk the natural biomechanical movement involves reaching forward with the head and neck. A hand that holds a fixed contact and does not allow that forward reach creates a restriction the horse escapes by popping the head up rather than reaching forward and down into the contact. Lack of preparation before the transition is the third cause. A transition asked without adequate preparation produces a horse that is caught unprepared and unbalanced. An unprepared horse raises his head as part of the startle and reorganization response to an unexpected demand — improving the quality of preparation dramatically reduces head popping for horses whose issue is primarily preparation-based.
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Watch: Why Does My Horse Pop Its Head Up During Transitions

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Warwick Schiller: Benefits of Teaching a Horse to Back Up — Why a Horse Pops Its Head Up During Transitions
Warwick Schiller