Pulmonary embolism (PE) is a fatal disease that arises from genetic and environmental factors. There is little evidence for low high-density lipoprotein cholesterol (HDL-C) with hyperhomocysteinemia to lead to PE. Therefore, we evaluated homocysteine levels and lipid profile in PE patients and to display risk for PE. Forty six patients with proven PE and 46 healthy controls were included in the study. Homocysteine and serum lipid levels were calculated and compared in both groups. There were no significant differences between two groups in terms of total cholesterol, triglyceride, and low-density lipoprotein cholesterol. In PE group, HDL-C levels were found significantly lower in comparison to the control group (P = .004). Mean homocysteine levels were significantly higher in PE group than in the control group (P = .001). High-density lipoprotein cholesterol levels were significantly low in which homocysteine levels were high in the PE group. We thought that low HDL-C level with hyperhomocysteinemia is susceptible to PE.