Background: Breast Cancer (BC) is the most common cancer in women worldwide. Long non-coding RNAs (lncRNAs) are regulatory non-coding transcripts and longer than 200 nucleotides. lncRNAs can affect many biological and pathological processes and dysregulation of them is related and studied in many human diseases like, cancers. We performed this study to evaluate the probable functions of lncRNAs FOXD2-AS1 and LINC00968 in breast cancer. Methods: The tumor tissue and adjacent non-tumor tissue specimens of luminal A and B breast cancer (the most frequent subtypes of breast cancer) were used to analyze the expression of these two lncRNAs, using the qRT-PCR technique. Furthermore, two luminal A breast cancer cell lines, MCF7 and T47D, were used to evaluate the expression of FOXD2-AS1 and LINC00968 compared with control breast cell line, MCF10A. Because of the luminal subtypes are the most frequent subtypes of breast cancer and also the most common subtypes among breast cancer patients, the present study was generally focused on the luminal and breast cancer. Also, some in silico analyses were done according to some databases and software for better understanding about the potential functions of mentioned lncRNAs in breast cancer. Results: Our data indicated the significant upregulation and downregulation of FOXD2-AS1 and LINC00968, respectively, in tumor tissues and breast cancer cell lines (MCF7, T47D). The bioinformatic analyses confirmed the experimental results. FOXD2-AS1 expression was positively associated with p53 protein and LINC00968 expression was negatively associated with tumor stage and lymph node metastasis. According to our findings, LINC00968 might be function as a tumor suppressor gene in breast cancer and this lncRNA might function in some cellular signaling pathways, like PI3K/Akt and Ras signaling pathways based on the co-expressed genes, but more investigations are required. Conclusions: The two mentioned lncRNAs might play roles in breast cancer pathogenesis but more experimental studies are needed to explore the mechanisms of the functions of these two lncRNAs in breast cancer.