Slow transit constipation (STC) is a clinical syndrome characterized by the decreased urge to defecate and delayed colonic transit. We have performed a comprehensive transcriptome profiling of STC patients using high-throughput RNA sequencing technology, identifying 344 mRNAs (|log2FC| >1 and p-value < 0.05), 104 lncRNAs (|log2FC| >1 and p-value < 0.05), 35 miRNAs (|log2FC| >1 and p-value < 0.05) and 190 circRNAs (|log2FC| >1 and p-value < 0.001) whose expression is specifically deregulated in STC patients. Among these RNAs, circRNAs are a recently discovered class of regulatory RNAs that have emerged as critical biomarkers and regulators of various types of diseases. However, the expression profile and mechanisms underlying circRNAs in STC based on human specimens have not yet been explored. Hence, the difference of circRNAs expression profile in colon samples from patients with STC and healthy controls (6 STC and 6 normal controls) may afford a unique view for understanding the pathogenesis in STC.