Hair follicles contain several tissues and cell types that differentiate down distinct pathways to provide for growth, keratinization and the maintenance of the hair shaft. Electron microscopy is useful for examining the morphological characteristics of developing hair follicles, including special types of keratinization, the timing of keratinization, programmed cell death, cell adhesion and separation, cell movement and changes in organelles. Hair follicles are one of the more challenging targets for electron microscopic analysis, and the use of neonatal animals combined with careful treatment of the samples can yield informative photomicrographs. Detailed protocols and examples of a number of techniques are presented here.