Our results show that CD4/CD8 ratio (OR 1.409, 95% CI 1.045–1.901, p = 0.025) and autoimmune disease (OR 0.264, 95% CI 0.133–0.524, p < 0.001) are independent risk factors for the bronchiectasis patients complicated with pulmonary embolism, but not homocysteine (OR 0.999, 95% CI 0.994–1.005, p = 0.827) (Table 4). The gene discussed is CD4; the disease is autoimmune disease.