Changes in the expression of cornified envelope (CE) proteins are thought to affect the development and course of atopic dermatitis (AD). The aim of this study was to examine the expression level of CE proteins in order to identify new molecular markers of the AD phenotype. Expression levels of CE proteins were evaluated in the skin of patients with AD (38 biopsies) and healthy subjects (26 biopsies). Levels of FLG, FLG2 and SPRR3 mRNAs and proteins were reduced in AD skin. Levels of LELP-1 and SPRR1A transcripts and proteins were significantly increased in AD skin. SPRR3v2 mRNA level in non-lesional AD skin correlated with severity of AD, and SPRR3 protein level in non-lesional AD skin correlated inversely with pruritus. FLG protein level in AD skin correlated inversely with severity of AD. These results point to SPRR3 as an important factor in AD and itch.