Bronchoalveolar lavage (BAL) is a well-tolerated diagnostic procedure in ILD. BAL cytology analyses (differential cell counts) should be considered in the evaluation of patients with IPF at the discretion of the treating physician based on availability and experience at their institution. BAL may reveal alternative specific diagnoses: malignancy, infections, eosinophilic pneumonia, histiocytosis X, or alveolar proteinosis. In the evaluation of patients with suspected IPF, the most important application of BAL is in the exclusion of other diagnoses. Prominent lymphocytosis (>30%) generally allows excluding a diagnosis of IPF.

According to the updated 2011 guidelines, in the absence of a typical UIP pattern on HRCT, a surgical lung biopsy is required for confident diagnosis.

Histologic specimens for the diagnosis of IPF must be taken at least in three different places and be large enough that the pathologist can comment on the underlying lung architecture. Small biopsies, such as those obtained via transbronchial lung biopsy (performed during bronchoscopy) are usually not sufficient for this purpose. Hence, larger biopsies obtained surgically via a thoracotomy or thoracoscopy are usually necessary.

Lung tissue from people with IPF usually show a characteristic histopathologic UIP pattern and is therefore the pathologic counterpart of IPF. Although a pathologic diagnosis of UIP often corresponds to a clinical diagnosis of IPF, a UIP histologic pattern can be seen in other diseases as well, and fibrosis of known origin (rheumatic diseases for example). There are four key features of UIP including interstitial fibrosis in a ‘patchwork pattern’, interstitial scarring, honeycomb changes and fibroblast foci.

Fibroblastic foci are dense collections of myofibroblasts and scar tissue and, together with honeycombing, are the main pathological findings that allow a diagnosis of UIP.

Raised inflammatory markers (high ESR, CRP) are common but nonspecific. Examination of the coughed up mucus is important in any lung infection and often reveals mixed bacterial flora. Transtracheal or transbronchial (via bronchoscopy) aspirates can also be cultured. Fiber optic bronchoscopy is often performed to exclude obstructive lesion; it also helps in bronchial drainage of pus.

Airway obstruction may cause obstructive pneumonitis or post-obstructive pneumonitis.

In restrictive lung disease, both forced expiratory volume in one second (FEV1) and forced vital capacity (FVC) are reduced, however, the decline in FVC is more than that of FEV1, resulting in a higher than 80% FEV1/FVC ratio.

In obstructive lung disease however, the FEV1/FVC is less than 0.7, indicating that FEV1 is significantly reduced when compared to the total expired volume. This indicates that the FVC is also reduced, but not by the same ratio as FEV1.

One definition requires a total lung capacity which is 80% or less of the expected value.

Most cases respond to antibiotics and prognosis is usually excellent unless there is a debilitating underlying condition. Mortality from lung abscess alone is around 5% and is improving.

Testing for miliary tuberculosis is conducted in a similar manner as for other forms of tuberculosis, although a number of tests must be conducted on a patient to confirm diagnosis. Tests include chest x-ray, sputum culture, bronchoscopy, open lung biopsy, head CT/MRI, blood cultures, fundoscopy, and electrocardiography. The tuberculosis (TB) blood test, also called an Interferon Gamma Release Assay or IGRA, is a way to diagnose latent TB.

A variety of neurological complications have been noted in miliary tuberculosis patients—tuberculous meningitis and cerebral tuberculomas being the most frequent. However, a majority of patients improve following antituberculous treatment. Rarely lymphangitic spread of lung cancer could mimic miliary pattern of tuberculosis on regular chest X-ray.

The tuberculin skin test, commonly used for detection of other forms of tuberculosis, is not useful in the detection of miliary tuberculosis. The tuberculin skin test fails due to the high numbers of false negatives. These false negatives may occur because of higher rates of tuberculin anergy compared to other forms of tuberculosis.

In disorders that are intrinsic to the lung parenchyma, the underlying process is usually pulmonary fibrosis (scarring of the lung). As the disease progresses, the normal lung tissue is gradually replaced by scar tissue interspersed with pockets of air. This can lead to parts of the lung having a honeycomb-like appearance.

Chest radiographs (X-ray photographs) often show a pulmonary infection before physical signs of atypical pneumonia are observable at all.

This is occult pneumonia. In general, occult pneumonia is rather often present in patients with pneumonia and can also be caused by "Streptococcus pneumoniae", as the decrease of occult pneumonia after vaccination of children with a pneumococcal vaccine suggests.

Infiltration commonly begins in the perihilar region (where the bronchus begins) and spreads in a wedge- or fan-shaped fashion toward the periphery of the lung field. The process most often involves the lower lobe, but may affect any lobe or combination of lobes.

Lower airway obstruction is mainly caused by increased resistance in the bronchioles (usually from a decreased radius of the bronchioles) that reduces the amount of air inhaled in each breath and the oxygen that reaches the pulmonary arteries. It is different from airway restriction (which prevents air from diffusing into the pulmonary arteries because of some kind of blockage in the lungs). Diseases that cause lower airway obstruction are termed obstructive lung diseases.

Lower airway obstruction can be measured using spirometry. A decreased FEV1/FVC ratio (versus the normal of about 80%) is indicative of an airway obstruction, as the normal amount of air can no longer be exhaled in the first second of expiration. An airway restriction would not produce a reduced FEV1/FVC ratio, but would reduce the vital capacity. The ventilation is therefore affected leading to a ventilation perfusion mismatch and hypoxia.

Extrapulmonary restriction is a type of restrictive lung disease, indicated by decreased alveolar ventilation with accompanying hypercapnia. It is characterized as an inhibition to the drive to breathe, or an ineffective restoration of the drive to breathe.

Extrapulmonary restriction can be caused by central and peripheral nervous system dysfunctions, over-sedation, or trauma (such as a broken rib).

If left untreated, miliary tuberculosis is almost always fatal. Although most cases of miliary tuberculosis are treatable, the mortality rate among children with miliary tuberculosis remains 15 to 20% and for adults 25 to 30%. One of the main causes for these high mortality rates includes late detection of disease caused by non-specific symptoms. Non-specific symptoms include: coughing, weight loss, or organ dysfunction. These symptoms may be implicated in numerous disorders, thus delaying diagnosis. Misdiagnosis with tuberculosis meningitis is also a common occurrence when patients are tested for tuberculosis, since the two forms of tuberculosis have high rates of co-occurrence.

Mycoplasma is found more often in younger than in older people.

Older people are more often infected by Legionella.

The Mantoux tuberculin skin test is often used to screen people at high risk for TB. Those who have been previously immunized may have a false-positive test result. The test may be falsely negative in those with sarcoidosis, Hodgkin's lymphoma, malnutrition, and most notably, active tuberculosis. Interferon gamma release assays, on a blood sample, are recommended in those who are positive to the Mantoux test. These are not affected by immunization or most environmental mycobacteria, so they generate fewer false-positive results. However, they are affected by "M. szulgai", "M. marinum", and "M. kansasii". IGRAs may increase sensitivity when used in addition to the skin test, but may be less sensitive than the skin test when used alone.

Diagnosing active tuberculosis based only on signs and symptoms is difficult, as is diagnosing the disease in those who are immunosuppressed. A diagnosis of TB should, however, be considered in those with signs of lung disease or constitutional symptoms lasting longer than two weeks. A chest X-ray and multiple sputum cultures for acid-fast bacilli are typically part of the initial evaluation. Interferon-γ release assays and tuberculin skin tests are of little use in the developing world. Interferon gamma release assays (IGRA) have similar limitations in those with HIV.

A definitive diagnosis of TB is made by identifying "M. tuberculosis" in a clinical sample (e.g., sputum, pus, or a tissue biopsy). However, the difficult culture process for this slow-growing organism can take two to six weeks for blood or sputum culture. Thus, treatment is often begun before cultures are confirmed.

Nucleic acid amplification tests and adenosine deaminase testing may allow rapid diagnosis of TB. These tests, however, are not routinely recommended, as they rarely alter how a person is treated. Blood tests to detect antibodies are not specific or sensitive, so they are not recommended.

"M. pneumoniae" infections can be differentiated from other types of pneumonia by the relatively slow progression of symptoms. A positive blood test for cold-hemagglutinins in 50–70% of patients after 10 days of infection (cold-hemagglutinin-test should be used with caution or not at all, since 50% of the tests are false-positive), lack of bacteria in a Gram-stained sputum sample, and a lack of growth on blood agar.

PCR has also been used.

While antibiotics with activity specifically against "M. pneumoniae" are often used (e.g., erythromycin, doxycycline), it is unclear if these result in greater benefit than using antibiotics without specific activity against this organism in those with an infection acquired in the community.

Routine complete blood count (CBC), basic metabolic profile, liver enzymes, and coagulation should be performed. Most experts recommend a diagnostic paracentesis be performed if the ascites is new or if the patient with ascites is being admitted to the hospital. The fluid is then reviewed for its gross appearance, protein level, albumin, and cell counts (red and white). Additional tests will be performed if indicated such as microbiological culture, Gram stain and cytopathology.

The "serum-ascites albumin gradient" (SAAG) is probably a better discriminant than older measures (transudate versus exudate) for the causes of ascites. A high gradient (> 1.1 g/dL) indicates the ascites is due to portal hypertension. A low gradient (< 1.1 g/dL) indicates ascites of non-portal hypertensive as a cause.

Ultrasound investigation is often performed prior to attempts to remove fluid from the abdomen. This may reveal the size and shape of the abdominal organs, and Doppler studies may show the direction of flow in the portal vein, as well as detecting Budd-Chiari syndrome (thrombosis of the hepatic vein) and portal vein thrombosis. Additionally, the sonographer can make an estimation of the amount of ascitic fluid, and difficult-to-drain ascites may be drained under ultrasound guidance. An abdominal CT scan is a more accurate alternate to reveal abdominal organ structure and morphology.

"Penicillium marneffei" demonstrates in vitro susceptibility to multiple antifungal agents including ketoconazole, itraconazole, miconazole, flucytosine, and amphotericin B. Without treatment patients have a poor prognosis; death occur by liver failure as the fungus releases toxins in the bloodstream. The elevation of liver enzyme in the blood helps to establish a diagnosis.

Ascites exists in three grades:

- Grade 1: mild, only visible on ultrasound and CT

- Grade 2: detectable with flank bulging and shifting dullness

- Grade 3: directly visible, confirmed with the fluid wave/thrill test

A septic embolism can be difficult to identify, as it is often attributed to other disorders or infections of the body. As a result, it may wreak havoc with CT scans. It can also be confused with lymph nodules, considering the similarity in shape and size. However, septic emboli usually lodge in the heart valves, where there are no lymph nodes.

Diagnosis is usually made by identification of the fungi from clinical specimens. Biopsies of skin lesions, lymph nodes, and bone marrow demonstrate the presence of organisms on histopathology.

The most common symptoms are fever, skin lesions, anemia, generalized lymphadenopathy, and hepatomegaly.

Pneumocystosis is an infection by "Pneumocystis jirovecii"that primarily occurs as a pulmonary infection AIDS patients, with extrapulmonary involvement being uncommon but, if occurring in the skin, presenting most often as nodular growths in the auditory canal.

A septic embolism is a type of embolism that is infected with bacteria, resulting in the formation of pus. These may become dangerous if dislodged from their original location. Like other emboli, a septic embolism may be fatal.

One of the common microbes that can lead to widespread dissemination of septic emboli is "Fusobacterium necrophorum", a Gram negative anaerobic bacillus. Fusobacteria are commensal organisms in the oral cavity.

"F. necrophorum" and" F. nucleatum" are the most important among the non-spore forming anaerobic bacilli in causing human infections." F. necroporum" may occasionally cause septicaemia with metastatic abscesses (Lemierre's syndrome).

The acute phase (invasion and migration) may be marked by diarrhea, abdominal pain, fever, cough, urticaria, hepatosplenomegaly, pulmonary abnormalities, and eosinophilia. During the chronic phase, pulmonary manifestations include cough, expectoration of discolored sputum containing clumps of eggs, hemoptysis, and chest radiographic abnormalities. Extrapulmonary locations of the adult worms result in more severe manifestations, especially when the brain is involved." "Diagnosis is based on microscopic demonstration of eggs in stool or sputum, but these are not present until 2 to 3 months after infection. (Eggs are also occasionally encountered in effusion fluid or biopsy material.) Concentration techniques may be necessary in patients with light infections. Biopsy may allow diagnostic confirmation and species identification when an adult or developing fluke is recovered.

Paragonimiasis can commonly be misdiagnosed as tuberculosis.