Variations of the HLA-B gene increase the risk of developing ankylosing spondylitis, although it is not a diagnostic test. Those with the HLA-B27 variant are at a higher risk than the general population of developing the disorder. HLA-B27, demonstrated in a blood test, can occasionally help with diagnosis, but in itself is not diagnostic of AS in a person with back pain. Over 90% of people that have been diagnosed with AS are HLA-B27 positive, although this ratio varies from population to population (about 50% of African Americans with AS possess HLA-B27 in contrast to the figure of 80% among those with AS who are of Mediterranean descent).

The Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), developed in Bath (UK), is an index designed to detect the inflammatory burden of active disease. The BASDAI can help to establish a diagnosis of AS in the presence of other factors such as HLA-B27 positivity, persistent buttock pain which resolves with exercise, and X-ray or MRI-evident involvement of the sacroiliac joints. It can be easily calculated and accurately assesses the need for additional therapy; a person with AS with a score of four out of a possible 10 points while on adequate NSAID therapy is usually considered a good candidate for biologic therapy.

The Bath Ankylosing Spondylitis Functional Index (BASFI) is a functional index which can accurately assess functional impairment due to the disease, as well as improvements following therapy. The BASFI is not usually used as a diagnostic tool, but rather as a tool to establish a current baseline and subsequent response to therapy.

Diagnosis of JIA is difficult because joint pain in children can be from many other causes. No single test can confirm the diagnosis, and most physicians use a combination of blood tests, X-rays, and clinical presentation to make an initial diagnosis of JIA. The blood tests measure antibodies and the rheumatoid factor. Unfortunately, the rheumatoid factor is not present in all children with JIA. Moreover, in some cases, the blood work is somewhat normal. X-rays are obtained to ensure that the joint pain is not from a fracture, cancer, infection, or congenital abnormality.

In most cases, fluid from the joint is aspirated and analyzed. This test often helps in making a diagnosis of JIA by ruling out other causes of joint pain.

There is no definitive test to diagnose psoriatic arthritis. Symptoms of psoriatic arthritis may closely resemble other diseases, including rheumatoid arthritis. A rheumatologist (a doctor specializing in autoimmune diseases) may use physical examinations, health history, blood tests and x-rays to accurately diagnose psoriatic arthritis.

Factors that contribute to a diagnosis of psoriatic arthritis include the following:

- Psoriasis in the patient, or a family history of psoriasis or psoriatic arthritis.

- A negative test result for rheumatoid factor, a blood factor associated with rheumatoid arthritis.

- Arthritis symptoms in the distal Interphalangeal articulations of hand (the joints closest to the tips of the fingers). This is not typical of rheumatoid arthritis.

- Ridging or pitting of fingernails or toenails (onycholysis), which is associated with psoriasis and psoriatic arthritis.

- Radiologic images demonstrating degenerative joint changes.

Other symptoms that are more typical of psoriatic arthritis than other forms of arthritis include enthesitis (inflammation in the Achilles tendon (at the back of the heel) or the plantar fascia (bottom of the feet)), and dactylitis (sausage-like swelling of the fingers or toes).

Some doctors include two other, less common forms: enthesitis-related arthritis and psoriatic JIA. Enthesitis is an inflammation of the insertion points of the tendons. This form occurs most often in boys older than 8, large joints of lower extremities are commonly affected; characteristically, it causes back pain, and is linked to ankylosing spondylitis and inflammatory bowel disease. Psoriatic JIA occurs most often in girls, in conjunction with psoriasis or any two of these features - i.e. dactylitit and nail pitting, although joint problems may precede the skin manifestations by several years.

FDG positron emission tomography (PET) may be useful to detect the condition early. Other imaging studies including MRI, CT scans, and X-rays may reveal inflammation and/or damaged cartilage facilitating diagnosis.

There are several clinical criteria used to diagnose this disease. McAdam "et al." introduced the clinical criteria for RP in 1976. These clinical criteria have later been expanded by Damiani "et al." in 1979 and finally Michet "et al." modified them in 1986. See the following table for these diagnostic clinical criteria and the number of conditions required for an official diagnosis.

Seventy percent of people who develop psoriatic arthritis first show signs of psoriasis on the skin, 15 percent develop skin psoriasis and arthritis at the same time, and 15 percent develop skin psoriasis following the onset of psoriatic arthritis.

Psoriatic arthritis can develop in people who have any level severity of psoriatic skin disease, ranging from mild to very severe.

Psoriatic arthritis tends to appear about 10 years after the first signs of psoriasis. For the majority of people, this is between the ages of 30 and 55, but the disease can also affect children. The onset of psoriatic arthritis symptoms before symptoms of skin psoriasis is more common in children than adults.

More than 80% of patients with psoriatic arthritis will have psoriatic nail lesions characterized by nail pitting, separation of the nail from the underlying nail bed, ridging and cracking, or more extremely, loss of the nail itself (onycholysis).

Enthesitis is observed in 30 to 50% of patients and most commonly involves the plantar fascia and Achilles’ tendon, but it may cause pain around the patella, iliac crest, epicondyles,

and supraspinatus insertions

Men and women are equally affected by this condition. Like psoriasis, psoriatic arthritis is more common among Caucasians than African or Asian people.

Assessment of Spondylarthritis International Society (ASAS criteria) is used for classification of axial spondyloarthritis (to be applied for patients with back pain greater than or equal to 3 months and age of onset less than 45 years). It is of two broad types:

1. Sacroiliitis on imaging plus 1 SpA feature, or

2. HLA-B27 plus 2 other SpA features

Sacroiliitis on imaging:

- Active (acute) inflammation on MRI highly suggestive of SpA-associated sacroiliitis and/or

- Definite radiographic sacroiliitis

SpA features:

- Inflammatory back pain

- Arthritis

- Enthesitis

- Anterior uveitis

- Dactylitis

- Psoriasis

- Crohn's disease or ulcerative colitis

- Good response to NSAIDs

- Family history of SpA

- HLA-B27

- Elevated CRP

Worldwide prevalence of spondyloarthropathy is approximately 1.9%.

There is no specific pathological testing or technique available for the diagnosis of the disease, although the International Study Group criteria for the disease are highly sensitive and specific, involving clinical criteria and a pathergy test. Behçet's disease has a high degree of resemblance to diseases that cause mucocutaneous lesions such as "Herpes simplex" labialis, and therefore clinical suspicion should be maintained until all the common causes of oral lesions are ruled out from the differential diagnosis.

Visual acuity, or color vision loss with concurrent mucocutaneous lesions or systemic Behçet's disease symptoms should raise suspicion of optic nerve involvement in Behçet's disease and prompt a work-up for Behçet's disease if not previously diagnosed in addition to an ocular work-up. Diagnosis of Behçet's disease is based on clinical findings including oral and genital ulcers, skin lesions such as erythema nodosum, acne, or folliculitis, ocular inflammatory findings and a pathergy reaction. Inflammatory markers such ESR, and CRP may be elevated. A complete ophthalmic examination may include a slit lamp examination, optical coherence tomography to detect nerve loss, visual field examinations, fundoscopic examination to assess optic disc atrophy and retinal disease, fundoscopic angiography, and visual evoked potentials, which may demonstrate increased latency. Optic nerve enhancement may be identified on Magnetic Resonance Imaging (MRI) in some patients with acute optic neuropathy. However, a normal study does not rule out optic neuropathy. Cerebrospinal fluid (CSF) analysis may demonstrate elevated protein level with or without pleocytosis. Imaging including angiography may be indicated to identify dural venous sinus thrombosis as a cause of intracranial hypertension and optic atrophy.

According to the International Study Group guidelines, for a patient to be diagnosed with Behçet's disease, the patient must have oral (aphthous) ulcers (any shape, size, or number at least 3 times in any 12 months period) along with 2 out of the following 4 "hallmark" symptoms:

- eye inflammation (iritis, uveitis, retinal vasculitis, cells in the vitreous)

- genital ulcers (including anal ulcers and spots in the genital region and swollen testicles or epididymitis in men)

- pathergy reaction (papule >2 mm dia. 24–48 hrs or more after needle-prick). The pathergy test has a specificity of 95 percent to 100 percent, but the results are often negative in American and European patients

- skin lesions (papulo-pustules, folliculitis, erythema nodosum, acne in post-adolescents not on corticosteroids)

Despite the inclusive criteria set forth by the International Study Group, there are cases where not all the criteria can be met and therefore a diagnosis cannot readily be made. There is however a set of clinical findings that a physician can rely upon in making a tentative diagnosis of the disease; essentially Behçet's disease does not always follow the International Study Group guidelines and so a high degree of suspicion for a patient who presents having any number of the following findings is necessary:

- arthritis/arthralgia

- cardio-vascular problems of an inflammatory origin

- changes of , psychoses

- deep vein thrombosis

- epididymitis

- extreme exhaustion

- inflammatory problems in chest and lungs

- mouth ulcers

- nervous system symptoms

- problems with hearing or balance

- stomach or bowel inflammation

- superficial thrombophlebitis

- any other members of the family with a diagnosis of Behçet's disease.

Oligoarthritis (from Greek "oligos" - 'few') is defined as arthritis affecting two to four joints during the first six months of disease.

The initial diagnostic workup for ulcerative colitis includes the following:

- A complete blood count is done to check for anemia; thrombocytosis, a high platelet count, is occasionally seen

- Electrolyte studies and renal function tests are done, as chronic diarrhea may be associated with hypokalemia, hypomagnesemia and pre-renal failure.

- Liver function tests are performed to screen for bile duct involvement: primary sclerosing cholangitis.

- X-ray

- Urinalysis

- Stool culture, to rule out parasites and infectious causes.

- Erythrocyte sedimentation rate can be measured, with an elevated sedimentation rate indicating that an inflammatory process is present.

- C-reactive protein can be measured, with an elevated level being another indication of inflammation.

- Sigmoidoscopy a type of endoscopy which can detect the presence of ulcers in the large intestine after a trial of an enema.

Although ulcerative colitis is a disease of unknown causation, inquiry should be made as to unusual factors believed to trigger the disease.

The simple clinical colitis activity index was created in 1998 and is used to assess the severity of symptoms.

In 1989, Brazilian researchers Professors Domingos Baggio (an entomologist from the Biomedical Sciences Institute of the University of São Paulo), Paulo Yasuda (a microbiologist from the same institute) and Natalino Hajime Yoshinari (a physician from the Rheumatology Department at University of São Paulo's Medical School) started research on Lyme disease in Brazil, by suggestion of Dr. Allen Steere. At that time, LD was almost unknown among Brazilian physicians.

The first cases were described in Brazil in 1992 in siblings from Cotia, São Paulo that developed symptoms as a migrating redness, general flu-like symptoms and arthritis after being bitten by ticks. Although the symptoms were similar to those presented by patients of Lyme disease, clinical and laboratorial results were considerably different. Ticks of the "Ixodes ricinus" complex were not found at the risk areas; bacteria from the "Borrelia burgdorferi" sensu lato complex —that cause Lyme disease— were not found in biological fluids and tissues of the siblings. Blood analysis of the patients on electron microscopy exhibited structures resembling microorganisms of the spirochaete phylum. For these reasons, the Brazilian zoonosis was considered a new disease and named Baggio–Yoshinari Syndrome (BYS), defined as: "Exotic and emerging Brazilian infectious disease, transmitted by ticks not belonging to the "Ixodes ricinus" complex, caused by latent spirochetes with atypical morphology, which originates LD-like symptoms, except for occurrence of relapsing episodes and auto-immune disorders".

Biopsies of the mucosa are taken to definitively diagnose UC and differentiate it from Crohn's disease, which is managed differently clinically. Microbiological samples are typically taken at the time of endoscopy. The pathology in ulcerative colitis typically involves distortion of crypt architecture, inflammation of crypts (cryptitis), frank crypt abscesses, and hemorrhage or inflammatory cells in the lamina propria. In cases where the clinical picture is unclear, the histomorphologic analysis often plays a pivotal role in determining the diagnosis and thus the management. By contrast, a biopsy analysis may be indeterminate, and thus the clinical progression of the disease must inform its treatment.

The Baggio–Yoshinari syndrome (BYS), formerly known as the Brazilian Lyme-like disease and Brazilian human borreliosis, is a disease transmitted by the "Amblyomma cajennense" tick, but the organism that causes the infection is still unknown. Clinical features resemble those of Lyme disease (LD).