Exploring gender-specific metabolic differences in biofluids provides a basic understanding of the physiological and metabolic phenotype of healthy subjects. Many reports have shown gender-specific metabolome profiles in the urine and serum of healthy subjects; however, limited studies focusing on exhaled human breath are available in the literature. In this study, we profiled the exhaled breath (~450 mL) volatile organic compounds (VOCs) of 47 healthy volunteers (age: 19-47; 23 male (M) and 24 female (F)) using a multidimensional gas chromatography and mass spectrometry and employed chemometric analysis to identify gender-specific VOCs. Eleven exhaled breath VOCs were identified from both uni and multivariate analysis from a training set (M = 15, F = 15) that could differentiate the genders within a healthy population. A partial least-squares discriminate analysis (PLS-DA) model built using these putative markers showed high accuracy in predicting (area under the receiver operating characteristic curve >0.9) a hold out/test sample set (n = 17). The outcomes of this report open up new avenues to undertake larger studies to elucidate the association of exhaled breath metabolites with gender-specific disease phenotypes and pharmacokinetics in the future.