Recent studies suggest that long non-coding RNAs (lncRNAs) play crucial roles in many types of human malignant cancers. However, the function of lncRNAs in benign tumors remains poorly understood. In the present study, to explored the potential roles of lncRNAs in benign epithelial ovarian cysts (BEOCs) which commonly occur in young women and possess malignant potential, we described the expression profile of the lncRNAs between BEOC and normal ovarian tissues using lncRNA microarray techniques. The results showed that 1,325 transcripts of lncRNAs (1,014 upregulated and 311 downregulated) were differentially expressed in the BEOCs compared with the normal controls [absolute fold-change ≥2, false discovery rate (FDR) <0.05]. We also conducted quantitative real-time PCR (qPCR) to confirm the microarray data. The results of qPCR revealed that the expression trend of 6 randomly selected lncRNAs was consistent with the microarray data. Furthermore, candidate lncRNAs were characterized by pathway analysis and Gene Ontology (GO). The present study is the first to demonstrate different expression profiles of lncRNAs between BEOCs and normal ovarian tissues. These lncRNAs may play a crucial role in the pathological process of BEOCs.