Various embodiments include methods for diagnosing and treating medical conditions that involve an autoimmune response to connective tissue such as collagen found in organs such as the lung. In one method pulmonary disease and disorders such as Idiopathic Pulmonary Fibrosis (IPF) are diagnosed by analyzing fluid or tissue samples obtained from a patient for evidence of an autoimmune response to various types of collagen including, for example, Type V. One type of assay for evidence of an autoimmune response to Type V collagen comprises the steps of obtaining a fluid or tissue sample from a patient, contacting at least a portion of the sample with antigen to anti-Type V collagen antibody and monitoring the mixture of sample and antigen for changes indicative of the presence of anti-Type V collagen in the sample. Another embodiment includes treating pulmonary diseases such as IPF by administering a therapeutically effective dose of epitopes of various collagens including Type V collagen.