Cholesteatoma is a pathologically benign but clinically destructive middle ear disease, which is caused by excessive epidermal migration and uncontrolled hyperproliferation of keratinocytes of squamous epithelium, leading to various clinical manifestations and serious complications, such as hearing loss, dizziness, facial paralysis, meningitis, and hydrocephalus. However, the pathogenesis of cholesteatoma is still not fully understood. Herein, we performed microarray analysis to identify the differentially expressed patterns of lncRNAs in cholesteatoma for the first time. Our data indicated that compared with matched normal skin tissue, lncRNA expression profiles were significantly altered in cholesteatoma. A total of 787 lncRNAs were identified (fold change ≥2.0, P<0.05), consisting of 181 upregulated and 606 downregulated lncRNAs. Furthermore, by constructing an lncRNA/miRNA/mRNA competing endogenous RNA (ceRNA) network, we found that lncRNAs, such as lncRNA‑uc001kfc.1, had ceRNA potential in cholesteatoma formation. In conclusion, lncRNAs were aberrantly expressed in cholesteatoma compared with normal skin tissues and may play important roles in cholesteatoma formation. Our findings shed novel light on the molecular mechanism of cholesteatoma pathogenesis and suggest that lncRNAs may be potential therapeutic targets for cholesteatoma.