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.

Some authors feel that all hepatocellular adenoma should be resected, because of the risk of rupture causing bleeding and because they may contain malignant cells. Current recommendations are that all hepatic adenomas should be resected, as long as they are surgically accessible and the patient is a reasonable operative candidate. Patients with adenomas should avoid oral contraceptives or hormonal replacement therapy.

Pregnancy could cause the adenoma to grow faster, so patients with hepatic adenomas should avoid pregnancy.

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

The standard of care for mucinous adenocarcinoma with clinical condition PMP involves cytoreductive surgery (CRS) with hyperthermic intraperitoneal chemotherapy (HIPEC), by surgical oncologists who specialize in treating PMP. Some surgeons also apply early post-operative intraperitonial chemotherapy (EPIC), adjunct to surgical cytoreduction and HIPEC. In situations where surgery is not required immediately, patients can be monitored via CT scans, tumor marker laboratory tests, and physical symptoms, to determine when, and if, surgery is warranted. Although some surgical procedures may be rather extensive, patients can and do recover from surgery, and the majority of these patients can and do live productive lives.

In debulking, the surgeon attempts to remove as much tumor as possible. CRS or cytoreductive surgery involves surgical removal of the peritoneum and any adjacent organs which appear to have tumor seeding. Since the mucus tends to pool at the bottom of the abdominal cavity, it is common to remove the ovaries, fallopian tubes, uterus, and parts of the large intestine. Depending upon the spread of the tumor, other organs might be removed, including but not limited to the gallbladder, spleen, and portions of the small intestine and/or stomach. For organs that cannot be removed safely (like the liver), the surgeon strips off the tumor from the surface.

Treatment is variable, both due to its rarity and to its frequently slow-growing nature. Treatment ranges from watchful waiting to debulking and hyperthermic intraperitoneal chemotherapy (HIPEC, also called intraperitoneal hyperthermic chemotherapy, IPHC) with cytoreductive surgery.

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

Wide, radical, complete surgical excision is the treatment of choice, with free surgical margins to achieve the best outcome and lowest chance of recurrence. Radiation is only used for palliation. In general, there is a good prognosis, although approximately 50% of patients die from disease within 3–10 years of presentation.

There are three main treatments for Hürthle cell adenomas. Once the adenoma is detected most often the nodules removed to prevent the cells from later metastisizing. A total thyroidectomy is often performed, this results in a complete removal of the thyroid. Some patients may only have half of their thyroid removed, this is known as a thyroid lobectomy. Another treatment option includes pharmacological suppression of thyroid hormone. The thyroid gland is responsible for producing the thyroid hormones triiodothyronine (T3) and thyroxine (T4). Patients with suppressed thyroid function often require oral thyroid replacement (e.g. levothyroxine) in order to maintain normal thyroid hormone levels. The final treatment option is RAI abaltion (radioactive iodine ablation). This treatment option is used to destroy infected thyroid cells after total thyroidectomy. This treatment does not change prognosis of disease, but will diminish the recurrence rate. Also, Hürthle cells do not respond well to RAI. However, often doctors suggest this treatment to patients with Hürthle cell adenoma and Hürthle cell carcinoma because some Hürthle cells will respond and it will kill remaining tissue.

Nipple adenomas are non-cancerous growths, which can recur if not completely surgically removed. There are reported cases of cancers arising within nipple adenomas, and following excision of nipple adenomas, but these are rare occurrences.

In localized, resectable adult GISTs, if anatomically and physiologically feasible, surgery is the primary treatment of choice. Surgery can be potentially curative, but watchful waiting may be considered in small tumors in carefully selected situations. Post-surgical adjuvant treatment may be recommended. Lymph node metastases are rare, and routine removal of lymph nodes is typically not necessary. Laparoscopic surgery, a minimally invasive abdominal surgery using telescopes and specialized instruments, has been shown to be effective for removal of these tumors without needing large incisions. The clinical issues of exact surgical indications for tumor size are controversial. The decision of appropriate laparoscopic surgery is affected by tumor size, location, and growth pattern.

Radiotherapy has not historically been effective for GISTs and GISTs do not respond to most chemotherapy medications, with responses in less than 5%. However, three medications have been identified for clinical benefit in GIST: imatinib, sunitinib, and regorafenib.

Imatinib (Glivec/Gleevec), an orally administered drug initially marketed for chronic myelogenous leukemia based on bcr-abl inhibition, also inhibits both "c-kit" tyrosine kinase mutations and PDGFRA mutations other than D842V, is useful in treating GISTs in several situations. Imatinib has been used in selected neoadjuvant settings. In the adjuvant treatment setting, the majority of GIST tumors are cured by surgery, and do not need adjuvant therapy. However, a substantial proportion of GIST tumors have a high risk of recurrence as estimated by a number of validated risk stratification schemes, and can be considered for adjuvant therapy. The selection criteria underpinning the decision for possible use of imatinib in these settings include a risk assessment based on pathological factors such as tumor size, mitotic rate, and location can be used to predict the risk of recurrence in GIST patients. Tumors <2 cm with a mitotic rate of <5/50 HPF have been shown to have lower risk of recurrence than larger or more aggressive tumors. Following surgical resection of GISTs, adjuvant treatment with imatinib reduces the risk of disease recurrence in higher risk groups. In selected higher risk adjuvant situations, imatinib is recommended for 3 years.

Imatinib was approved for metastatic and unresectable GIST by the US FDA, February 1, 2002. The two-year survival of patients with advanced disease has risen to 75–80% following imatinib treatment.

If resistance to imatinib is encountered, the multiple tyrosine kinase inhibitor sunitinib (marketed as Sutent) can be considered.

The effectiveness of imatinib and sunitinib depend on the genotype. cKIT- and PDGFRA-mutation negative GIST tumors are usually resistant to treatment with imatinib as is neurofibromatosis-1-associated wild-type GIST. A specific subtype of PDGFRA-mutation, D842V, is also insensitive to imatinib.

Regorafenib (Stivarga) was FDA approved in 2013 for advanced GISTs that cannot be surgically removed and that no longer respond to imatinib (Gleevec) and sunitinib (Sutent).

Most patients with thyroid adenoma can be managed by watchful waiting (without surgical excision) with regular monitoring. However, some patients still choose surgery after being fully informed of the risks. Regular monitoring mainly consists of watching for changes in nodule size and symptoms, and repeat ultrasonography or needle aspiration biopsy if the nodule grows.

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.

Even though there is no evidence of malignant potential, transurethral resection is recommended together with long-term antibiotic prophylaxis for at least one year after resection. Prolonged antibiotic therapy is suggested due to the frequent finding of UTI as an associated or causative factor.

Symptoms of short bowel syndrome are usually addressed with medication. These include:

- Anti-diarrheal medicine (e.g. loperamide, codeine)

- Vitamin, mineral supplements and L-glutamine powder mixed with water

- H2 blocker and proton pump inhibitors to reduce stomach acid

- Lactase supplement (to improve the bloating and diarrhoea associated with lactose intolerance)

In 2004, the USFDA approved a therapy that reduces the frequency and volume of total parenteral nutrition (TPN), comprising: NutreStore (oral solution of glutamine) and Zorbtive (growth hormone, of recombinant DNA origin, for injection) together with a specialized oral diet. In 2012, an advisory panel to the USFDA voted unanimously to approve for treatment of SBS the agent teduglutide, a glucagon-like peptide-2 analog developed by NPS Pharmaceuticals, who intend to market the agent in the United States under the brandname Gattex. Teduglutide had been previously approved for use in Europe and is marketed under the brand Revestive by Nycomed.

Surgical procedures to lengthen dilated bowel include the Bianchi procedure, where the bowel is cut in half and one end is sewn to the other, and a newer procedure called serial transverse enteroplasty (STEP), where the bowel is cut and stapled in a zigzag pattern. Heung Bae Kim, MD, and Tom Jaksic, MD, both of Children's Hospital Boston, devised the STEP procedure in the early 2000s. The procedure lengthens the bowel of children with SBS and may allow children to avoid the need for intestinal transplantation. As of June 2009, Kim and Jaksic have performed 18 STEP procedures. The Bianchi and STEP procedures are usually performed by pediatric surgeons at quaternary hospitals who specialize in small bowel surgery.

Patients treated with complete surgical excision can expect an excellent long term outcome without any problems. Recurrences may be seen in tumors which are incompletely excised.

A non-minimally invasive Hürthle cell carcinoma is typically treated by a total thyroidectomy followed by radioactive iodine therapy. A Hürthle cell adenoma or a minimally invasive tumor can be treated by a thyroid lobectomy, although some surgeons will perform a total thyroidectomy to prevent the tumor from reappearing and metastasizing.

A modified radical neck dissection may be performed for clinically positive lymph nodes.

The tumor must be removed with as complete a surgical excision as possible. In nearly all cases, the ossicular chain must be included if recurrences are to be avoided. Due to the anatomic site of involvement, facial nerve paralysis and/or paresthesias may be seen or develop; this is probably due to mass effect rather than nerve invasion. In a few cases, reconstructive surgery may be required. Since this is a benign tumor, no radiation is required. Patients experience an excellent long term outcome, although recurrences can be seen (up to 15%), especially if the ossicular chain is not removed. Although controversial, metastases are not seen in this tumor. There are reports of disease in the neck lymph nodes, but these patients have also had other diseases or multiple surgeries, such that it may represent iatrogenic disease.

If the anemia is severe, blood transfusion is required before any other intervention is considered. Endoscopic treatment is an initial possibility, where cautery or argon plasma coagulation (APC) treatment is applied through the endoscope. Failing this, angiography and emolization with particles is another microinvasive treatment option, which avoids the need for surgery and bowel resection. Here, the vessel supplying the angiodysplasia is selectively catheterized and embolizaed with microparticles. Resection of the affected part of the bowel may be needed if the other modalities fail. However, the lesions may be widespread, making such treatment impractical.

If the bleeding is from multiple or inaccessible sites, systemic therapy with medication may be necessary. First-line options include the antifibrinolytics tranexamic acid or aminocaproic acid. Estrogens can be used to stop bleeding from angiodysplasia. Estrogens cause mild hypercoaguability of the blood. Estrogen side effects can be dangerous and unpleasant in both sexes. Changes in voice and breast swelling is bothersome in men, but older women often report improvement of libido and perimenopausal symptoms. (The worries about hormone replacement therapy/HRT, however, apply here as well.)

In difficult cases, there have been positive reports about octreotide and thalidomide.

In severe cases or cases not responsive to either endoscopic or medical treatment, surgery may be necessary to arrest the bleeding.

The "treat empirically" route also has its difficulties, which have all come under wide debate and study. Recommendations are varied but seem to find some common ground around the notion that treatment should be individualized to the specific circumstances under which a patient has developed BLS since these circumstances affect the complex microbial make up of the affected bowel.

Tetracyclines have been the mainstay of treatment for BLS, but recent studies have concluded Rifaximin to be very effective in the treatment of BLS. One study by Di Stefano et al., however, concluded Metronidazole to be more effective than Rifaximin in the treatment of BLS.

Surgical management is reserved for fixing anatomical causes of bowel obstruction that interfere with normal function once they are amenable to such intervention. These conditions include:

- Strictures

- Fistulae

- Diverticula

Benign myoepithelioma are treated with simple excision. They are less prone to recurrence than pleomorphic adenoma.

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.

Villous adenoma is a type of polyp that grows in the colon and other places in the gastrointestinal tract and sometimes in other parts of the body. These adenomas may become malignant (cancerous). Villous adenomas have been demonstrated to contain malignant portions in about one third of affected persons, and invasive malignancy in another one third of removed specimens. Colonic resection may be required for large lesions. These can also lead to secretory diarrhea with large volume liquid stools with few formed elements. They are commonly described as secreting large amounts of mucus, resulting in hypokalaemia in patients. On endoscopy a "cauliflower' like mass is described due to villi stretching. Being an adenoma, the mass is covered in columnar epithelial cells.

Treatment options depend on the type of tumor and on its size:

- Prolactinomas are most often treated with cabergoline or quinagolide (both dopamine agonists), which decrease tumor size as well as alleviates symptoms, followed by serial imaging to detect any increase in size. Treatment where the tumor is large can be with radiation therapy or surgery, and patients generally respond well. Efforts have been made to use a progesterone antagonist for the treatment of prolactinomas, but so far have not proved successful.

- Somatotrophic adenomas respond to octreotide, a long-acting somatostatin analog, in many but not all cases according to a review of the medical literature. Unlike prolactinomas, thyrotrophic adenomas characteristically respond poorly to dopamine agonist treatment.

- Surgery is a common treatment for pituitary tumors. The normal approach is Trans-sphenoidal adenectomy, which usually can remove the tumor without affecting the brain or optic nerves.

- Danazol is a steroid compound that has been labelled as an "Anterior pituitary suppressant".

The appropriate treatment in contemporary western medicine is complete surgical excision of the abnormal growth with a small amount of normal surrounding breast tissue.