Your doctor may examine your abdomen and perform an internal (vaginal) examination.

http://www.patient.co.uk/health/ovarian-cyst-leaflet

How is an ovarian cyst diagnosed?

As most ovarian cysts cause no symptoms, many cysts are diagnosed by chance - for example, during a routine examination, or if you have an ultrasound scan for another reason.
If you have symptoms suggestive of an ovarian cyst, your doctor may examine your abdomen and perform an internal (vaginal) examination. He or she may be able to feel an abnormal swelling which may be a cyst.