Treatment for FAP depends on the genotype. Most individuals with the APC mutation will develop colon cancer by the age of 40, although the less-common attenuated version typically manifests later in life (40–70). Accordingly, in many cases, prophylactic surgery may be recommended before the age of 25, or upon detection if actively monitored. There are several surgical options that involve the removal of either the colon or both the colon and rectum.

- Rectum involved: the rectum and part or all of the colon are removed. The patient may require an ileostomy (permanent stoma where stool goes into a bag on the abdomen) or have an ileo-anal pouch reconstruction. The decision to remove the rectum depends on the number of polyps in the rectum as well as the family history. If the rectum has few polyps, the colon is partly or fully removed and the small bowel (ileum) can be directly connected to the rectum instead (ileorectal anastomosis).

- Rectum not involved: the portion of the colon manifesting polyps can be removed and the ends 'rejoined' (partial colectomy), a surgery that has a substantial healing time, but leaves quality of life largely intact.

Prophylactic colectomy is indicated if more than a hundred polyps are present, if there are severely dysplastic polyps, or if multiple polyps larger than 1 cm are present.

Treatment for the two milder forms of FAP may be substantially different from the more usual variant, as the number of polyps are far fewer, allowing more options.

Various medications are being investigated for slowing malignant degeneration of polyps, most prominently the non-steroidal anti-inflammatory drugs (NSAIDs). NSAIDS have been shown to significantly decrease the number of polyps but do not usually alter management since there are still too many polyps to be followed and treated endoscopically.

Prior to reaching the advanced stages of colorectal cancer, the polyps are confined to the inner wall and thickness of the intestinal tract and do not metastasize or 'spread'. So provided FAP is detected and controlled either at the pre-cancerous stage or when any cancerous polyps are still internal to the intestinal tract, surgery has a very high success rate of preventing or removing cancer, without recurrence, since the locations giving rise to cancer are physically removed "in toto" by the surgery.

Following surgery, if a partial colectomy has been performed, colonoscopic surveillance of the remaining colon is necessary as the individual still has a risk of developing colon cancer. However, if this happened, it would be a fresh incident from polyps developing anew in the unremoved part of the colon subsequent to surgery, rather than a return or metastasis of any cancer removed by the original surgery.

Resection of the polyps is required only if serious bleeding or intussusception occurs. Enterotomy is performed for removing large, single nodules. Short lengths of heavily involved intestinal segments can be resected. Colonoscopy can be used to snare the polyps if they are within reach.

People with juvenile polyps may require yearly upper and lower endoscopies with polyp excision and cytology. Their siblings may also need to be screened regularly. Malignant transformation of polyps requires surgical colectomy.

Polyps can be removed during a colonoscopy or sigmoidoscopy using a wire loop that cuts the stalk of the polyp and cauterises it to prevent bleeding. Many "defiant" polyps—large, flat, and otherwise laterally spreading adenomas—may be removed endoscopically by a technique called endoscopic mucosal resection (EMR), which involves injection of fluid underneath the lesion to lift it and thus facilitate surgical excision. These techniques may be employed as an alternative to the more invasive colectomy.

Surgery remains the front-line therapy for HNPCC. There is an ongoing controversy over the benefit of 5-fluorouracil-based adjuvant therapies for HNPCC-related colorectal tumours, particularly those in stages I and II.

Treatment:wide excision taking 8mm normal tissue as this is locally malignant. For recurrence radiotherapy is given

The first line of treatment for nasal polyps is topical steroids. Steroids decrease the inflammation of the sinus mucosa to decrease the size of the polyps and improve symptoms. Topical preparations are preferred in the form of a nasal spray, but are often ineffective for people with many polyps. Steroids by mouth often provide drastic symptom relief, but should not be taken for long periods of time due to their side effects. Because steroids only shrink the size and swelling of the polyp, people often have recurrence of symptoms once the steroids are stopped. Decongestants do not shrink the polyps, but can decrease swelling and provide some relief. Antibiotics are only recommended if the person has a co-occurring bacterial infection.

In people with nasal polyps caused by aspirin or NSAIDs, avoidance of these medications will help with symptoms. Aspirin desensitization has also been shown to be beneficial.

Treatment may consist of watching and waiting, complete surgical removal, radiation therapy, antiestrogens (ex. Tamoxifen), NSAIDs, chemotherapy or microwave ablation.

Patients with desmoid tumors should be evaluated by a multi-disciplinary team of surgeons, medical oncologists, radiation oncologists, geneticists and nurses. There is no cure for desmoid tumors and when possible patients are encouraged to enlist in clinical trials.

A biopsy is always indicated as the definitive method to determine nature of the tumour. Management of these lesions is complex, the main problem being the high rates of recurrence in FAP associated disease. Conversely, for intra-abdominal fibromatosis without evidence of FAP, although extensive surgery may still be required for local symptoms, the risk of recurrence appears to be lower. Wide surgical resection with clear margins is the most widely practiced technique with radiation, chemotherapy, or hormonal therapy being used to reduce the risk of recurrence.

Current experimental studies are being done with Gleevec (Imatinib) and Nexavar (sorafenib) for treatment of desmoid tumors, and show promising success rates.

Polyps are either pedunculated (attached to the intestinal wall by a stalk) or sessile (grow directly from the wall).

Endoscopic sinus surgery with removal of polyps is often very effective for most people providing rapid symptom relief. Endoscopic sinus surgery is minimally-invasive and is done entirely through the nostril with the help of a camera. Surgery should be considered for those with complete nasal obstruction, uncontrolled runny nose, nasal deformity caused by polyps or continued symptoms despite medical management. Surgery serves to remove the polyps as well as the surrounding inflamed mucosa, open obstructed nasal passages, and clear the sinuses. This not only removes the obstruction caused by the polyps themselves, but allows medications such as saline irrigations and topical steroids to become more effective.

Surgery lasts approximately 45 minutes to 1 hour and can be done under general or local anesthesia. Most patients tolerate the surgery without much pain, though this can vary from patient to patient. The patient should expect some discomfort, congestion, and drainage from the nose in the first few days after surgery, but this should be mild. Complications from endoscopic sinus surgery are rare, but can include bleeding and damage to other structures in the area including the eye or brain.

Many physicians recommend a course of oral steroids prior to surgery to reduce mucosal inflammation, decrease bleeding during surgery, and help with visualization of the polyps. Nasal steroid sprays should be used preventatively after surgery to delay or prevent recurrence. People often have recurrence of polyps even following surgery. Therefore, continued follow up with a combination of medical and surgical management is preferred for the treatment of nasal polyps.

Complete removal of a SSA is considered curative.

Several SSAs confer a higher risk of subsequently finding colorectal cancer and warrant more frequent surveillance. The surveillance guidelines are the same as for other colonic adenomas. The surveillance interval is dependent on (1) the number of adenomas, (2) the size of the adenomas, and (3) the presence of high-grade microscopic features.

Immunohistochemistry is now being used more often to diagnose patients likely to have Muir–Torre syndrome. Sebaceous neoplasms are only infrequently encountered, and immunohistochemistry is reliable and readily available, so researchers have recommended its use. Routine immunohistochemical detection of DNA mismatch repair proteins help identify hereditary DNA mismatch repair deficiency.

Treatment of Muir–Torre syndrome normally consists of oral isotretinoin. The drug has been found to prevent tumor development.

Patients with Muir–Torre syndrome should follow the same stringent screening for colorectal carcinoma and other malignancies as patients with Lynch syndrome. This includes frequent and early colonoscopies, mammograms, dermatologic evaluation, and imaging of the abdomen and pelvis.

Surgical removal of the tumor, adjuvant chemotherapy prior to tumor removal, and liver transplantation have been used to treat these cancers. Primary liver transplantation provides high, long term, disease-free survival rate in the range of 80%, in cases of complete tumor removal and adjuvant chemotherapy survival rates approach 100%. The presence of metastases is the strongest predictor of a poor prognosis.

Treatment is mainly surgical; radiotherapy or chemotherapy is usually an indication of relapse. Head and neck desmoid fibromatosis is a serious condition due to local aggression, specific anatomical patterns and the high rate of relapse. For children surgery is particularly difficult, given the potential for growth disorders.

Treatment includes prompt radical excision with a wide margin and/or radiation. Despite their local infiltrative and aggressive behavior, mortality is minimal to nonexistent for peripheral tumours. In intra-abdominal fibromatosis associated with Familial adenomatous polyposis (FAP), surgery is avoided if possible due to high rates of recurrence within the abdomen carrying significant morbidity and mortality. Conversely, for intra-abdominal fibromatosis without evidence of FAP extensive surgery may still be required for local symptoms, but the risk of recurrence is low.

Polyps on the vocal folds can take on many different forms, and can sometimes result from vocal abuse, although this is not always the cause. They can occur on one or both vocal folds, and appear as swelling, a bump (similar to a nodule), a stalk-like growth, or a blister-like lesion. Most polyps are larger than nodules, which are more similar to callouses on the vocal folds.

Polyps and nodules can exhibit similar symptoms including hoarseness or breathiness, “rough” or “scratchy” voice, harshness in vocal quality, shooting pain from ear to ear, sensation of having “a lump in the back of the throat”, neck pain, decreased pitch range in the voice, and vocal and bodily fatigue.

If an individual experiences symptoms for more than 2 to 3 weeks, they should see a physician. For a diagnosis, a thorough evaluation of the voice should include a physical examination, preferably by an otolaryngologist (ear, nose, and throat doctor) who specializes in voice, a voice evaluation with a speech-language pathologist (SLP), a neurological examination (in certain cases)

The qualities of the voice that will be evaluated include quality, pitch, loudness, and ability to sustain voicing. In some cases, an instrumental examination may be performed with an endoscope into the mouth or nose; this gives a clear look at the vocal folds and larynx in general. In addition to this, a stroboscope (flashing light) may be used to observe the movement of the vocal folds during speech.

Polyps may be treated with medical, surgical, or behavioral intervention. Surgical intervention involves removing the polyp from the vocal fold. This approach is only used when the growth(s) are very large, or have existed for an extended amount of time. In children, surgical intervention is rare. Existing medical problems may be treated in an effort to reduce the strain and negative impact on the vocal cords. This could include treatment for gastrointestinal reflux disease, allergies, and thyroid problems. Intervention to stop smoking and reduce stress may also be needed. Most people receive behavioral intervention, or vocal therapy, from an SLP. This might involve teaching good vocal hygiene, and reducing or stopping vocal abuse behaviors. Direct voice treatments may be used to alter pitch, loudness, or breathe support to promote good voicing.

Some benign tumors need no treatment; others may be removed if they cause problems such as seizures, discomfort or cosmetic concerns. Surgery is usually the most effective approach and is used to treat most benign tumors. In some case other treatments may be of use. Adenomas of the rectum may be treated with sclerotherapy, a treatment in which chemicals are used to shrink blood vessels in order to cut off the blood supply. Most benign tumors do not respond to chemotherapy or radiation therapy, although there are exceptions; benign intercranial tumors are sometimes treated with radiation therapy and chemotherapy under certain circumstances. Radiation can also be used to treat hemangiomas in the rectum. Benign skin tumors are usually surgically resected but other treatments such as cryotherapy, curettage, electrodesiccation, laser therapy, dermabrasion, chemical peels and topical medication are used.

There is a risk of development of cancer with fundic gland polyposis, but it varies based on the underlying cause of the polyposis. The risk is highest with congenital polyposis syndromes, and is lowest in acquired causes. As a result, it is recommended that patients with multiple fundic polyps have a colonoscopy to evaluate the colon. If there are polyps seen on colonoscopy, genetic testing and testing of family members is recommended.

In the gastric adenocarcinoma associated with proximal polyposis of the stomach (GAPPS), there is a high risk of early development of proximal gastric adenocarcinoma.

It is still unclear which patients would benefit with surveillance gastroscopy, but most physicians recommend endoscopy every one to three years to survey polyps for dysplasia or cancer. In the event of high grade dysplasia, polypectomy, which is done through the endoscopy, or partial gastrectomy may be recommended. One study showed the benefit of NSAID therapy in regression of gastric polyps, but the efficacy of this strategy (given the side effects of NSAIDs) is still dubious.

Most of these tumors are treated with surgical removal. It is non recurrent.

Primary treatment for this cancer, regardless of body site, is surgical removal with clean margins. This surgery can prove challenging in the head and neck region due to this tumour's tendency to spread along nerve tracts. Adjuvant or palliative radiotherapy is commonly given following surgery. For advanced major and minor salivary gland tumors that are inoperable, recurrent, or exhibit gross residual disease after surgery, fast neutron therapy is widely regarded as the most effective form of treatment.

Chemotherapy is used for metastatic disease. Chemotherapy is considered on a case by case basis, as there is limited trial data on the positive effects of chemotherapy. Clinical studies are ongoing, however.

Most juvenile polyps are benign, however, malignancy can occur. The cumulative lifetime risk of colorectal cancer is 39% in patients with juvenile polyposis syndrome.

Treatment may include the following:

- Surgery with or without radiation

- Radiotherapy

Fast neutron therapy has been used successfully to treat salivary gland tumors, and has shown to be significantly more effective than photons in studies treating unresectable salivary gland tumors.

- Chemotherapy

Some suggestions for surveillance for cancer include the following:

- Small intestine with small bowel radiography every 2 years,

- Esophagogastroduodenoscopy and colonoscopy every 2 years,

- CT scan or MRI of the pancreas yearly,

- Ultrasound of the pelvis (women) and testes (men) yearly,

- Mammography (women) from age 25 annually livelong, and

- Papanicolaou smear (Pap smear) every year

Follow-up care should be supervised by a physician familiar with Peutz–Jeghers syndrome. Genetic consultation and counseling as well as urological and gynecological consultations are often needed.

Fundic gland polyposis is a medical syndrome where the fundus and the body of the stomach develop many polyps. The condition has been described both in patients with familial adenomatous polyposis (FAP) and attenuated variants (AFAP), and in patients in whom it occurs sporadically.

Overall, the mainstay of the treatment for salivary gland tumor is surgical resection. Needle biopsy is highly recommended prior to surgery to confirm the diagnosis. More detailed surgical technique and the support for additional adjuvant radiotherapy depends on whether the tumor is malignant or benign.

Surgical treatment of parotid gland tumors is sometimes difficult, partly because of the anatomical relationship of the facial nerve and the parotid lodge, but also through the increased potential for postoperative relapse. Thus, detection of early stages of a tumor of the parotid gland is extremely important in terms of prognosis after surgery.

Generally, benign tumors of the parotid gland are treated with superficial(Patey's operation) or total parotidectomy with the latter being the more commonly practiced due to high incidence of recurrence. The facial nerve should be preserved whenever possible. The benign tumors of the submandibular gland is treated by simple excision with preservation of mandibular branch of the trigeminal nerve, the hypoglossal nerve, and the lingual nerve. Other benign tumors of minor salivary glands are treated similarly.

Malignant salivary tumors usually require wide local resection of the primary tumor. However, if complete resection cannot be achieved, adjuvant radiotherapy should be added to improve local control. This surgical treatment has many sequellae such as cranial nerve damage, Frey's syndrome, cosmetic problems, etc.

Usually about 44% of the patients have a complete histologic removal of the tumor and this refers to the most significant survival rate.