Objectives: To measure the extent to which gender differences in poor lipid control among individuals at risk for cardiovascular diseases could be explained by patient-level characteristics. Study Design: Cross-sectional analyses of merged Veteran Health Administration (VHA) and Medicare claims data for the fiscal years (FY) 2002 and 2003 consisting of veterans using VHA facilities and were diagnosed with diabetes or heart disease or hypertension during FY 2002 and had recorded LDL cholesterol values in FY2003 (N = 527,568). There were 10,582 women and 516,986 men veterans. Poor lipid control was defined as LDL cholesterol values ≥130 mg/dL. Multivariate techniques consisted of logistic regressions. Based on the parameter estimates and distribution of individual characteristics, we used a decomposition technique to analyze factors that contributed to the gender difference in poor lipid control. Principal Findings: A significantly higher percent of women (27.4%) than men (17.1%) had LDL cholesterol values ≥130 mg/dL. Of the 10.3 percentage point difference in lipid control, 3.4 percentage points were explained by variables included in the model. The gender difference in poor lipid control was mostly explained by age, physical illnesses, use of lipid lowering medications and depression. Conclusions: Only one-third of the gender difference in poor lipid control could be explained by differences in individual characteristics, some of which are modifiable or could be used to identify groups at risk with poor lipid control. Our findings suggest that gender differences in lipid control could be partially reduced by increasing the prescription of lipid lowering drugs and treating depression among women. Interventions that improve lipid control in the non-elderly will also benefit women. However the largest part of the difference in lipid control between women and men remains unexplained and further research is needed to identify additional modifiable and unmodifiable factors.