This study aimed to compare Apolipoprotein B(Apo B) with non-HDL-C as a predictor and discriminating factor of acute coronary syndrome (ACS). This is a case control study among 50 cases of first attack of ACS among 18-45 years of age of both sex, admitted in coronary care unit of Mymensingh Medical College Hospital, Bangladesh from June 2009 to May 2010. Data was recently reanalyzed. Apo B is more sensitive than non-HDL C (84% vs. 62%) as well with more negative predictive value (NPV) (76.5% vs. 62.7%) but with similar positive predictive value (PPV) (63%). Specificity was more for non HDL C than Apo B (64% vs. 52%). Highest specificity and PPV observed for HDL- C, 88% and 71.4% respectively but with low sensitivity (30%). In this study diagnostic value of LDL-C, TC and TG was low. Apo B was a more discriminating factor as well predictor for ACS cases than non-HDL-C (OR: 5.678, 95% CI 2.227 - 14.528, P=0.001) vs. (OR: 2.901, 95% CI 1.288 - 6.534, P=0.01). Area under the Receiver Operating Characteristic (ROC) curve was greater for Apo B than non-HDL-C (0.680 vs. 0.630). Though ApoB and non-HDL-C theoretically often equally reflects the atherogenic burden, Apo B was a more discriminating factor for ACS cases than non-HDL-C.