The development of abiotic stress resistant cultivars is of premium importance for the agriculture of developing countries. Further progress in maize performance under stresses is expected by combining marker assisted breeding with metabolite markers. In order to dissect metabolic responses and to identify promising metabolite marker candidates, metabolite profiles of maize leaves were analysed and compared with grain yield in field trials. Plants were grown under well water conditions (control) or exposed to drought, heat and both stresses simultaneously. Trials were conducted in 2010 and 2011 using ten tropical hybrids selected to exhibit diverse abiotic stress tolerance. Drought stress invoked accumulation of many amino acids including isoleucine, valine, threonine and GABA which has been commonly reported in both field and greenhouse experiments in many plant species. Two photorespiratory amino acids, glycine and serine, and myo-inositol also accumulated under drought. Combination of drought and heat invoked relatively few specific responses and most of the metabolic changes were predictable from the sum of the responses to individual stresses. Statistical analysis revealed significant correlation between levels of glycine and myo-inositol and grain yield under drought. Levels of myo-inositol in control conditions were also related to grain yield under drought. Furthermore multiple linear regression models very well explained the variation of grain yield via the combination of several metabolites. These results indicate the importance of photorespiration and raffinose family oligosaccharide metabolism in grain yield under drought and suggest single or multiple metabolites as potential metabolic markers for breeding of abiotic stress tolerant maize.