Children with CGD are usually healthy at birth. The most common CGD infection in infancy is a skin or bone infection with the bacteria Serratia marcescens, so any infant with this particular infection should be tested for CGD. In fact, any infant or child with a significant infection with any of the organisms previously listed should be tested for CGD.

Infections in CGD may involve any organ or tissue, but the skin, lungs, lymph nodes, liver and bones are the usual sites of infection. Infections may rupture and drain with delayed healing and residual scarring. Infection of lymph nodes (under the arm, in the groin, in the neck) is a common problem in CGD, often requiring drainage or surgery along with antibiotics.

Pneumonia (infection of the lungs) is a common problem in CGD. Pneumonias due to the fungus Aspergillus may come on very slowly, initially only causing fatigue, and only later causing cough or chest pain. Fungal pneumonias often do not cause fever. In contrast, bacterial infections (Staphylococcus aureus, Burkholderia cepacia complex, Serratia marcescens, Nocardia) usually come on with fever and cough. Nocardia, in particular, can cause high fevers and lung abscesses that can destroy parts of the lung. It is important to identify the presence and specific cause of infections early and to treat the infection completely, usually for long periods of time, to ensure infection stops and prevent relapse. Chest X-rays and computerized tomography (CT) scans of the chest are the best ways to look for lung infections. When they are seen, it is very important to figure out exactly which infection it is and that may require a biopsy (usually done with a needle or a bronchoscope) or sometimes even surgery. Treatment may require many weeks.

Liver abscesses occur in about one third of individuals with CGD. A liver abscess can start out as fever and fatigue, but it may also cause pain over the right upper abdomen. Some sort of scan is required for diagnosis, such as magnetic resonance imaging (MRI), CT scan, or ultrasound, and needle biopsy is necessary to determine the specific cause of the infection. Staphylococcus aureus causes most liver abscesses in CGD. Liver abscesses are hard to drain and may need surgery, but treatment with a combination antibiotics and steroids reduces the inflammation and lets the antibiotics work better even without surgery.

Bone infection (osteomyelitis) can involve the hands and feet, and can also involve the spine, particularly if there is a fungal infection in the lungs that spreads to the spine. 

Newer antibiotics and antifungals are very active when administered by mouth. Managing infections and improving quality of life in individuals with CGD can be greatly improved with early diagnosis and appropriate therapy.

Inflammation is also a significant problem in people with CGD, both with and without infection. Granulomas can cause trouble with intestinal or urinary function, and can also form in the lung, the eye, or the skin.

One of the most difficult aspects of living with CGD is bowel inflammation. About 40-50% of individuals with CGD develop inflammation in the intestine that is not clearly due to a specific infection. Individuals with CGD can have severe abdominal pain, diarrhea, weight loss, and sometimes abnormal narrowing in parts of the intestines. Inflammation in the gastrointestinal (GI) tract can present as colitis (inflammation and ulcers of the bowl wall of the colon. Commonly called inflammatory bowel disease (IBD), this inflammation is similar in clinical appearance to Crohn’s disease. In addition, mouth sores, frequent vomiting, problems with urination and sometimes damage to the kidneys can be seen due to the inflammation associated with CGD. Treatment of this is similar to that applied to other forms of IBD, with steroids having good effect to control symptoms, but other immunosuppressive drugs are often used as steroid sparing agents. It is important to note that, injectable drugs that block the action of inflammatory molecule tumor necrosis factor alpha (TNFα), although very effective to reduce the IBD symptoms, can lead to severe infections in individuals with CGD and are not recommended.