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Aim and background Heart-type fatty acid-binding proteins (H-FABP) which are detected within 2–3 h of acute myocardial infarction are involved in uptake of free fatty acids in the myocardium. Our aim in the present study is to compare window periods of H-FABP to high sensitivity troponin T (hs-Trop T) in acute ST elevation myocardial infarction (STEMI). Methods 160 STEMI diagnosed patient’s serum samples are analyzed for hs-Trop T and H-FABP. Different window periods of chest pain onset (<3 h, 3–6 h and >6 h) are compared with complications, in-hospital mortality and statistically analyzed. Results From 160 patients, 53 (33%) cases are presented in <3 h, 75 (47%) in 3–6, and 32 (20%) after >6 h respectively. Accordingly sensitivity of hs-Trop T was 92%, 94% and 97% while H-FABP was 75%, 88% and 84%, respectively. Overall sensitivity was 94% and 82% respectively. Statistically significant difference between mean hs-Trop T values with respect to window period <3, 3–6 and >6 h was 0.21, 0.35 and 0.80 ng/ml respectively, p value < 0.0001. No significant difference in H-FABP values was observed. Hs-Trop T positively correlated with age ( r = 0.153, P = 0.05), window period ( r = 0.363, P < 0.0001), TIMI score ( r = 0.208, P = 0.008), ejection fraction ( r = 0.191, P = 0.008), serum H-FABP ( r = 0.229, P = 0.004), and serum hs-CRP ( r = 0.326, p < 0.001). There was a statistically significant difference of mean hs-Trop T values with or without in hospital mortality (0.35 vs. 0.85 ng/ml, respectively, p = 0.008). No significant correlation to age, TIMI score, ejection fraction and hs-CRP values for H-FABP was observed. Conclusion It appears that hs-Trop T is a more sensitive marker than H-FABP in early hours of AMI and higher hs-Trop T predicts increase in-hospital mortality. [ABSTRACT FROM AUTHOR]