Objective: To estimate the levels of myeloperoxidase in various stages of chronic kidney disease, and to correlate them with an inflammatory marker and lipid profile. Method: The cross-sectional study was conducted at the Biochemistry Department, Basic Medical Sciences Institute, in collaboration with the Nephrology Department, Jinnah Post Graduate Medical Centre, Karachi, from January 2013 to September 2014, and comprised chronic kidney disease patients and healthy controls. Serum cholesterol, triglycerides, high-density lipoprotein, C-reactive protein and myeloperoxidase levels were noted. Data was subjected to statistical analysis. Results: Of the 150 subjects, 84(56%) were cases and 66(44%) were controls. Weight, body mass index, triglycerides, very low-density lipoprotein, C-reactive protein and myeloperoxidase levels were significantly higher among the cases compared to the controls (p<0.05). Serum myeloperoxidase had a significantly positive association with C-reactive protein (p<0.01), cholesterol (p<0.01), triglycerides (p<0.01), low-density lipoprotein (p<0.01) and very low-density lipoprotein (p<0.01), and had a negative correlation with high-density lipoprotein (p<0.01). Conclusion: Myeloperoxidase concentration had association with lipid profile and C-reactive protein.