Since the practitioner's hands apply only gentle pressure to the skull, this noninvasive technique is virtually without danger to the patient. Cranial manipulation has existed as a therapy since the 1930s, when an American osteopath, William Garner Sutherland, first theorized that because the bones of the skull were not fused into a single piece but rather had seams and could be moved slightly, perhaps their manipulation could have some effect on a person's health. He then discovered that compression of the skull had an effect due to the pressure exerted on the cerebrospinal fluid that permanently surrounds and bathes the brain and spinal cord. He also postulated that this fluid has a natural, rise-and-fall rhythm of its own that an experienced hand can detect. He argued that the trained hand also could detect spots on the skull that cause points of restriction, leading to abnormal fluid rhythm. He believed that this irregular rhythm could lead to dysfunction and poor health.

Modern craniosacral therapists are trained to manipulate the meninges as well as the seams of the skull (and sometimes the bones of the face). These underlying meningeal membranes cover the brain and the entire length of the spinal cord, extending from the skull to the sacrum at the end of the spine. During a consultation, the practitioner usually will have the patient lie on a massage table and will palpate gently the patient's skull and spine. If the practitioner also is an osteopathic physician, a complete physical and case history is usually obtained before treating the patient. This touching is essential to the practitioner who must be able to "listen" with her hands to what is called the cranial rhythmic impulse. This pulsation is distinct from both the familiar cardiovascular pulse and the normal breathing rhythm. To the experienced practitioner, this pulse has a cycle of three seconds of inflow and three seconds of rest, averaging 10 cycles per minute. Interruption of the inflow by abnormal restrictions, such as from an injury, or by abnormal tension patterns may result in problems such as dizziness, migraine headaches, and sinus problems.