Deregulation of long noncoding RNAs (lncRNAs) is becoming recognized as a major feature of many neurological disorders. In the current study, we aimed to measure the expression of seven lncRNAs and lncRNA-targeted mRNAs in the peripheral lymphocytes of attention-deficit/hyperactivity disorder (ADHD), autism spectrum disorder (ASD), and intellectual disability (ID) patients via quantitative real-time reverse transcriptase PCR (qRT-PCR). We found that in ADHD, the expression of mRNAs of the BDNF, SHANK2, HOXB5, and HOXA6 genes was downregulated significantly, but there was no difference in the expression of selected lncRNAs. As for ASD, the expression of the mRNAs of the HOXA6 and HOXA13 genes was significantly down-regulated, accompanied by a significant reduction of lncRNA that overlaps with the gene locus of HOXA13. A gender-dependent difference in expression of lncRNAs and targeted mRNAs was indicated in ID. In male ID, there was a significantly downregulated expression of mRNAs of HOXB5 and HOXA13, accompanied by differentially decreased expression of lncRNA-targeted mRNAs of SYT15, PKNOX2, SHANK2, HOXB5, HOXA6, and HOXA13. In female ID, the mRNAs of HOXB5 and HOXA6 were significantly down-regulated, with the significantly down-regulated expression of lncRNA-targeted mRNAs of BDNF, PKNOX2, HOXB5, and HOXA6, and the differentially increased expression of lncRNAs that overlap SYT15 and SHANK2. Our results indicated a differential expression pattern for lncRNAs and targeted mRNAs in the peripheral lymphocytes in different neurological disorders.