After the sample is obtained from the affected area it is then examined by a pathologist in a laboratory. A pathologist is a physician that examines tissues, blood and body fluids in order to diagnose diseases. The sample arrives at the laboratory with relevant information regarding the patient together with a description of the site of the body from where the sample was collected. The pathologist examines the sample and then he/she makes a description of the tissue. The tissue is then preserved in an appropriate container.
 
Unfortunately in the case of mesothelioma it is difficult to diagnose the disease by just looking at the cells collected from the fluid around the lungs, abdomen or heart through a microscope. Testing of the fluid may produce inconclusive and unreliable results and so this has a limited value. It is also difficult to diagnose the disease from tissues collected by the use of the needle, because of the small sample size collected. When looking through a microscope; mesothelioma cells may resemble other type of cancers. For example it is difficult to distinguish between pleural Mesothelioma and lung cancer. Also, peritoneal mesothelioma cells and cells of cancers of the ovaries are also very similar, when looked at through a microscope. Hence needle biopsies are not an effective method in the diagnosis of mesothelioma. An electron microscope is a very powerful microscope that can magnify cells 100 times more than the normal microscope (light microscope). The electron microscope may so produce more reliable results.

However other tests and techniques are usually performed in order to distinguish mesothelioma from other type of cancers such as lung cancer. Immunohistochemistry is a test where cell types are identified based on different proteins on the surface of the cells. This techniques used in this test have the aim to recognize the types of chemicals (markers) that are contained in mesothelioma. In the past, the type of chemicals (markers) used to distinguish mesothlioma from lung cancer were ‘negative markers'. Pathologist watched for markers that were found in lung cancer and not in mesothelioma. So, if they were not present it meant that the individual didn't have lung cancer. This made the diagnosis difficult to confirm. Nowadays ‘positive markers' are used, where if certain markers are found, it means that the cells belong to mesothelioma. DNA Microarray analysis is a new test that can be performed in order to distinguish between different gene patterns of cancers.