Metabolomics may be defined as the analysis of thousands of naturally occurring small molecules (metabolites) such as sugars, organic acids, amino acids and nucleotides that are the products of cellular metabolism. As such, it is essentially the study of the complete biochemical phenotype (or metabotype) of any biofluid, cell, tissue or indeed organism, at both the qualitative and quantitative level. Metabolic profiles are context dependent, and will change in response to environmental circumstances. Therefore, while the technique has primarily been used in biomedical research to date, it is also applicable to ecological investigations and shows great promise in measuring the impact of factors such as climate change, disease, food restriction, infection and parasite load. In this review we detail the history and background of metabolomics and discuss examples of previous and potential future metabolic studies and applications in ecological science.