Our knowledge of the biological basis of schizophrenia has significantly increased with the contribution of in vivo proton and phosphorus magnetic resonance spectroscopy (MRS), a noninvasive tool that can assess the biochemistry from a localized region in the human body. Studies thus far suggest altered membrane phospholipid metabolism at the early stage of illness and reduced N-acetylaspartate, a measure of neuronal volume/viability in chronic schizophrenia. Inconsistencies remain in the literature, in part due to the complexities in the MRS methodology. These complexities of in vivo spectroscopy make it important to understand the issues surrounding the design of spectroscopy protocols to best address hypotheses of interest. This review addresses these issues, including 1) understanding biochemistry and the physiologic significance of metabolites; 2) the influence of acquisition parameters combined with spin-spin and spin-lattice relaxation effects on the MRS signal; 3) the composition of spectral peaks and the degree of overlapping peaks, including the broader underlying peaks; 4) factors affecting the signal-to-noise ratio; 5) the various types of localization schemes; and 6) the objectives to produce accurate and reproducible quantification results. The ability to fully exploit the potentials of in vivo spectroscopy should lead to a protocol best optimized to address the hypotheses of interest.