Usually the pus drains outside on to the skin surface.An infected pilonidal cyst is an abscess that requires incision and drainage in order to improve.The physician will then drain the pus and remove hair and any other debris from the wound. The wound is then packed with gauze and allowed to heal. Antibiotics are generally not necessary unless your physician feels that you have a spreading skin infection (cellulitis). Pain medication will often be prescribed.The complications of a pilonidal cyst include abscess formation,recurrence of the pilonidal cyst,systemic infection (infection that spreads throughout the body),rarely, squamous cell carcinoma (the development of a form of skin cancer within the cyst).Although 40%-50% of patients with pilonidal cysts will experience a recurrence, in general, the long-term prognosis is excellent.