Long non-coding RNAs (IncRNAs) have been established to participate in various biological processes that are crucial for development and differentiation. However, the roles of IncRNAs in the mechanisms of human bone marrow mesenchymal stem cells (MSCs) differentiation are not completely understood. The purpose of the study was to investigate the expression profiles of IncRNAs during the chondrogenic differentiation of human bone marrow MSCs, with a view to studying the biological function of IncRNAs and their involvement in the mechanism of differentiation. We compared the IncRNAs expression profiles of undifferentiated and differentiated cells during chondrogenic differentiation by microarray. 3638 differentially expressed IncRNAs were identified (fold-change >2.0 or <-2.0, P < 0.05), consisting of 2166 up-regulated and 1472 down-regulated. Microarray data were validated using quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Bioinformatic analyses were applied for further study of these differentially expressed IncRNAs. Among these IncRNAs, ZBED3-AS1 and CFA-941F9.9 were further analyzed with co-expression network and target prediction analysis. The results showed that the two up-regulated IncRNAs are likely to play important roles in chondrogenic differentiation process. In conclusion, the expression profile of IncRNAs was significantly altered during differentiation process. It provided a new insight on complicated regulation mechanisms of human bone marrow MSCs chondrogenic differentiation. (C) 2014 Elsevier Inc. All rights reserved.