A diagnosis can be made by an evaluation of medical history and clinical observation. The Beighton criteria are widely used to assess the degree of joint hypermobility. DNA and biochemical studies can help identify affected individuals. Diagnostic tests include collagen gene mutation testing, collagen typing via skin biopsy, echocardiogram, and lysyl hydroxylase or oxidase activity. However, these tests are not able to confirm all cases, especially in instances of an unmapped mutation, so clinical evaluation by a geneticist remains essential. If there are multiple affected individuals in a family, it may be possible to perform prenatal diagnosis using a DNA information technique known as a linkage study. There is poor knowledge about EDS among practitioners.

There are several disorders that share some characteristics with Ehlers–Danlos syndrome. For example, in cutis laxa the skin is loose, hanging, and wrinkled. In EDS, the skin can be pulled away from the body but is elastic and returns to normal when let go. In Marfan syndrome, the joints are very mobile and similar cardiovascular complications occur. People with EDS tend to have a "Marfanoid" appearance (e.g., tall, skinny, long arms and legs, "spidery" fingers). However, physical appearance and features in several types of Ehlers–Danlos syndrome also have characteristics including short stature, large eyes, and the appearance of a small mouth and chin, due to a small palate. The palate can have a high arch, causing dental crowding. Blood vessels can sometimes be easily seen through translucent skin, especially on the chest. The genetic connective tissue disorder, Loeys-Dietz Syndrome, also has symptoms that overlap with EDS.

In the past, Menkes disease, a copper metabolism disorder, was thought to be a form of Ehlers–Danlos syndrome. It is not uncommon for patients to be misdiagnosed with fibromyalgia, bleeding disorders or other disorders that can mimic EDS symptoms before a correct diagnosis is made. Because of these similar disorders and complications that can arise from an un-monitored case of EDS, a correct diagnosis is very important. Pseudoxanthoma elasticum (PXE) is worth consideration in diagnosing a patient.

As of July 2000, hypermobility was diagnosed using the Brighton criteria. The Brighton criteria do not replace the Beighton score but instead use the previous score in conjunction with other symptoms and criteria. HMS is diagnosed in the presence of either two major criteria, one major and two minor criteria, or four minor criteria. The criteria are:

For some people with hypermobility, lifestyle changes decrease symptom severity. In general activity that increases pain is to be avoided. For example:

- Typing can reduce pain from writing.

- Voice control software or a more ergonomic keyboard can reduce pain from typing.

- Bent knees or sitting can reduce pain from standing.

- Unwanted symptoms are frequently produced by some forms of yoga and weightlifting.

- Use of low impact elliptical training machines can replace high-impact running.

- Pain-free swimming may require a kickboard or extra care to avoid hyperextending elbow and other joints.

- Weakened ligaments and muscles contribute to poor posture, which may contribute to other medical conditions.

- Isometric exercise avoids hyperextension and contributes to strength.