Oxidative stress and apoptotic cell death are two important processes that occur under several disease states and in conditions of toxicant insult. Traditionally, investigators have chosen a variety of analytical methods to detect and/or quantify oxidative stress and apoptosis. The approach has proven less satisfying, however, when applied to complex systems with many unknown influences. Such areas of study could benefit from the development and application of new and more powerful analytical tools. Microarray-based approach has been developed for analyzing various cellular phenomena at the level of gene expression. These gene arrays are hybridization chips that are capable of simultaneous analysis of the expression of thousands of genes. Often, this approach warrants examining a multitude of unrelated genes which can greatly impede the interpretation of results. The real-time RT-PCR-based methodology presented here allows simultaneous detection and analysis of as many as 84 well-characterized genes associated with either oxidative stress or apoptosis in hypothalamic neuronal cells exposed to cholesterol secoaldehyde, an “ozone-/singlet oxygen-specific” oxidation product of cholesterol that has been shown to be present at the inflammatory sites including the arterial plaque and the brain specimens of patients with Alzheimer’s disease. This pathway-specific analysis of the expression of the well-defined chosen set of genes offers ways of convenient and reliable interpretation of results that often corroborate well with the results obtained from other standard biochemical analytical approaches.