It is impossible to understand keratinization disorders without knowing what is going on at molecular levels. We and others have been analyzing the issues of keratinization by means of (immuno)electron microscopy and found that this is quite a useful tool for molecular pathology. We summarize the recent advances in the biology and pathology of keratinization at ultrastructural and molecular levels. Tonofilaments, a morphological hallmark of keratinocytes, are composed of keratins. Epidermolytic hyperkeratosis, a genetic disease of keratin K1/K10, shows clumped tonofilaments that are shown to be actually composed of K1/K10 by immunoelectron microscopy. Distribution of profilaggrin and its derivatives has also been revealed by immunoelectron microscopy. Defective interaction between keratin and filaggrin is seen in epidermolytic hyperkeratosis. Transient nuclear localization of N-terminal domains of profilaggrin is observed in the transitional cells of normal epidermis. Unique distribution of trichohyalin was detected in psoriasis. Distribution of various components of cornified cell envelopes including involucrin and loricrin in normal and abnormal keratinization can also be detected with this technique. Premature formation of involucrin-rich cell envelopes are observed in psoriasis vulgaris. Defects in cross-linking of loricrin are detected in transglutaminase 1 knockout mice, the animal model of lamellar ichthyosis. Abnormal distribution of loricrin has been detected in genetic diseases of loricrin (loricrin keratoderma). By combining immunoelectron microscopy and terminal deoxynucleotidyl transferase-mediated dUDP nick-end labeling (TUNEL) methods, the nature of TUNEL positive cells has also been unravelled.