Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nt that are involved in cardiovascular diseases (CVDs). To determine whether lncRNAs are involved in stable angina pectoris (SAP), we analysed the expression profile of lncRNAs and mRNAs on a genome-wide scale in SAP of Uyghur population. Five pairs of SAP patients and healthy controls were screened by an Agilent microarray (human lncRNA + mRNA Array V4.0). Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the lncRNA expression levels in 50 SAP and 50 controls. Data analyses were performed using R and Bioconductor. A total of 1871 up- and 231 down-regulated lncRNAs were identified to be differentially expressed in the peripheral blood mononuclear cells (PBMCs). Microarray analysis results identified the lncRNAs NR_037652.1, ENST00000607654.1, ENST00000589524.1 and uc004bhb.3, which were confirmed by qRT-PCR. Among screened lncRNAs, the annotation result of their co-expressed mRNAs showed that the most significantly related pathways were the NF-κB signalling pathway, apoptosis and the p53 signalling pathway, while the main significantly related diseases were the cholesterol, calcium and coronary disease. Our study indicated that clusters of lncRNAs were significantly differentially expressed between SAP patients and matched controls. These lncRNAs may play a significant role in SAP development and could serve as biomarkers and potential targets for the future treatment of SAP.