A 48-year-old man who had a complaint of swelling in the left submandibular region and right side of the neck was referred to our radiology clinic for sonographic examination that revealed a type 1 hydatid cyst with a diameter of 32 mm in the left submandibular gland, and a type 3 hydatid cyst with a diameter of 33 mm in the right thyroid gland. The diagnosis was verified by computed tomography, magnetic resonance imaging, and hemagglutination tests. To the best of our knowledge, this is the second case in the literature of hydatid cysts involving both submandibular and thyroid glands. There was no abdominal, thoracic or brain involvement. The patient was a singer and did not accept surgical treatment, and percutaneous drainage with the PAIR (Puncture-Aspiration of cyst contents-Injection of hypertonic saline solution-Reaspiration) technique was performed for both cysts. There were no complications during or after the intervention. During 4 months of follow up the sizes of both cysts were decreased and the germinative membranes were shrunken, having a pseudotumor appearance. To the best of our knowledge, this is the first case in the literature that the PAIR method was applied for thyroid and submandibular gland hydatid cysts. Percutaneous treatment of thyroid and submandibular gland hydatid cysts seems to be a safe and effective procedure as a possible alternative to surgery.