There exist two primary classifications of polycythemia: primary and secondary polycythemia. These conditions share the common characteristic of an abnormally elevated concentration of hemoglobin and/or hematocrit within the peripheral blood. It's worth noting that secondary polycythemia is significantly influenced by smoking, a known factor that diminishes oxygen delivery to tissues. Furthermore, smoking's detrimental effects on oxidative stress, blood coagulation, and blood lipid composition amplify the risk of developing atherosclerotic diseases, thereby underscoring the importance of addressing this hazardous habit in the context of overall health and well-being. Aim: This study aims to illuminate the intricate relationship between smoking, lipid profiles, and reproductive hormones, shedding light on potential health implications and providing valuable data to inform clinical management strategies for individuals facing this condition. Material and Methods: A research investigation was carried out involving a cohort of 100 male participants, comprising 75 individuals diagnosed with polycythemia and 25 control subjects. The age range of the participants ranged from 20 to 59 years. Blood samples were procured from the blood bank in Maysan Province (in Iraq) and gathered during the period extending from November 2022 to March 2023. Results: The result showed that total cholesterol, triglyceride, low-density lipoprotein and very low-density lipoprotein increased significantly (p < 0.05). While high-density lipoprotein decreased significantly (p <0.05) in both groups of polycythemia (smokers and non-smokers) compared with the control group. No significant (p > 0.05) variation was recorded in the values of follicle-stimulating hormone, testosterone and estrogen in the smoker and non-smoker groups compared with the control group. The levels of luteinizing hormone in smoker and non-smoker groups were increased significantly (p ˂ 0.05) in comparison to the control group. Conclusion: Our investigation has revealed notable alterations in the lipid profiles of men affected by polycythemia, regardless of their smoking status. However, when it comes to changes in reproductive hormones within the studied population, these adjustments did not attain statistically significant levels, except for luteinizing hormone, which exhibited a noteworthy variation.