Diabetes mellitus (DM) is a progressive chronic disorder, which affects people belonging to all age groups of the population. This disease is accompanied by a greatly increased risk of cardiovascular death. In the present study, the effects of streptozotocin (STZ)-induced type 1 diabetes on apex myocardium of the rat heart have been investigated using Fourier Transform Infrared (FTIR) spectra. The cluster analysis has been applied to FTIR spectra to differentiate the diabetic samples from the normal controls. In addition, the protein secondary structures of diabetic and normal tissues were predicted by neural networks based on the amide I band of the FTIR spectra. The findings mainly suggest that 5 weeks of diabetes alters the lipid and protein profile of normal rat heart apex myocardium, which might have an important role in understanding the molecular mechanism of diabetes-related heart diseases. © 2007 - IOS Press and the authors. All rights reserved.