DCLK1 expression is critically required for maintaining growth of human colon cancer cells (hCCCs). Human colorectal tumors (CRCs) and hCCCs express a novel short isoform of DCLK1 (DCLK1-S) (isoform2) from β-promoter of hDCLK1-gene, while normal-colons express long-isoform (DCLK1-L) (isoform1) from 5′(α)-promoter, suggesting that DCLK1-S, and not DCLK1-L, marks cancer stem cells (CSCs). Even though DCLK1-S differs from DCLK1-L by only six amino-acids, we succeeded in generating a mono-specific DCLK1-S-Antibody (PS41014), which does not cross-react with DCLK1-L, and specifically detects CSCs. Sub-cellular localization of S/L isoforms was examined by immune-electron-microscopy (IEM). Surprisingly, besides plasma membrane and cytosolic fractions, S/L also localized to nuclear/mitochondrial fractions, with pronounced localization of S-isoform in the nuclei and mitochondria. Sporadic CRCs develop from adenomas. Screening colonoscopy is used for detection/resection of growths, and morphological/pathological criteria are used for risk assessment and recommendations for follow-up colonoscopy. But, these features are not precise and majority of the patients will never develop cancer. We hypothesized that antibody-based assay(s), which identify CSCs, will significantly improve prognostic value of morphological/pathological criteria. We conducted a pilot retrospective study with PS41014-Ab, by staining archived Adenoma specimens from patients who developed (High-risk) or did not develop (Low-risk) adenocarcinomas within 10–15 years. PS41014-Ab stained Adenomas from initial and follow-up colonoscopies of high-risk patients, at significantly higher levels (3–5 fold) than Adenomas from low-risk patients, suggesting that PS41014-Ab could be used as an additional tool for assessing CRC risk. CRC patients, with high DCLK1-S expressing tumors (by qRT-PCR), were reported to have worse overall survival than low-expressers. We now report that DCLK1-S specific Ab may help to identify high-risk patients at the time of index/screening colonoscopy.