ulceration of the genital mucous membranes, eye lesions or digestive problems, swollen glands in neck (lymphadenopathy) or a  general unwell feeling.The diagnosis comes mostly from the history and examination, but the following special investigations may be involved: blood tests (vitamin deficiency, anemia, leukemia, Epstein-Barr virus, HIV infection, diabetes) microbiological swabs (infection), or urinalysis (diabetes). A biopsy (minor procedure to cut out a small sample of the ulcer to look at under a microscope) with or without immunofluorescence may be required, to rule out cancer, but also if a systemic disease is suspected. Ulcers caused by local trauma are painful to touch and sore. They usually have an irregular border with erythematous margins and the base is yellow. As healing progresses, a keratotic (thickened, white mucosa) halo may occur. : 52

Differential diagnosis
Due to various factors (saliva, relative thinness of oromucosa, trauma from teeth, chewing, etc. ), vesicles and bullae which form on the mucous membranes of the oral cavity tend to be fragile and quickly break down to leave ulcers. Aphthous stomatitis and local trauma are very common causes of oral ulceration; the many other possible causes are all rare in comparison. Traumatic ulceration
Most mouth ulcers that are not associated with recurrent aphthous stomatitis are caused by local trauma. The mucous membrane lining of the mouth is thinner than the skin, and easily damaged by mechanical, thermal (heat/cold), chemical, or electrical means, or by irradiation.
An ulcer is a deeper breach of epithelium compared to an erosion or excoriation, and involves damage to both epithelium and lamina propria.An erosion is a superficial breach of the epithelium, with little damage to the underlying lamina propria. A mucosal erosion is an erosion which specifically occurs on a mucous membrane. Only the superficial epithelial cells of the epidermis or of the mucosa are lost, and the lesion can reach the depth of the basement membrane. Erosions heal without scar formation.Excoriation is a term sometimes used to describe a breach of the epithelium which is deeper than an erosion but shallower than an ulcer. This type of lesion is tangential to the rete pegs and shows punctiform (small pinhead spots) bleeding, caused by exposed capillary loops. Causes
Ulcers and erosions can be the result of a spectrum of conditions including:

Those causing auto-immune epithelial damage, damage because of an immune defect (e.g., HIV, leukemia)
Infections (e.g. herpes viruses)
Nutritional disorders (e.g., vitamin deficiencies). Chemicals such as SLS (a common ingredient in many toothpastes) have been linked to mouth ulcers, and have been recognized by public health agencies such as the NHS as a risk factor. Injuries (e.g. biting of the lip, tongue, and cheek, hard foods can scrape the oral tissues, hot foods can cause burns)
Stress: When the body is stressed, the immune symptom may trigger mouth sores

Pathophysiology
The exact pathogenesis is dependent upon the cause.