Abstract Background Pancreatic cysts may be detected in 40 to 50 percent of patients who undergo abdominal magnetic resonance imaging for unrelated reasons. Mucinous cysts such as intraductal papillary mucinous neoplasms (IPMN) and mucinous cystic neoplasms (MCN) are known precursor lesions of pancreatic ductal adenocarcinoma. Therefore, it is imperative to identify mucinous cysts from nonmucinous cysts. In addition to cytology analysis, biomarker analysis in cyst fluid obtained by endoscopic ultrasound-guided fine needle aspiration can also provide information for the differential diagnosis of a mucinous cyst. Carcinoembryonic antigen (CEA) has been used as the biomarker to differentiate mucinous and nonmucinous pancreatic cysts with a sensitivity of around 63% and specificity of around 88%. Recently, glucose in pancreatic cyst fluid has been shown to have a better sensitivity (92%) and specificity (87%) in the differentiation of mucinous cysts using a threshold of <50 mg/dL. Therefore, it is consequential for clinical laboratories to validate glucose tests in pancreatic cyst fluid samples. In this study, we report the validation of the glucose test in pancreatic cyst fluid samples using the glucose assay on an automated chemistry analyzer. Methods The glucose assay, GLUC3, on Roche Cobas c702 analyzer was used to measure glucose in pancreatic cyst fluid samples. For linearity and recovery studies, cyst fluid samples were spiked with stock glucose solutions of known concentrations in a way that the spiked fluid samples always contained no less than 90% of the cyst fluid. Linearity was determined by assaying nine samples with glucose concentrations from 0–718 mg/dL. For the recovery study, various amounts of glucose were added to a cyst fluid sample containing undetectable glucose. The expected glucose concentrations in these samples are 23.2, 46.4, 92.7, and 159 mg/dL, respectively. Intra-run and inter-run precisions were determined by measuring glucose ten times in a run and in 10 separated runs, respectively, in 9 cyst fluid samples containing various amounts of glucose ranging from 0–718 mg/dL. The effect of hemoglobin was tested by spiking one cyst fluid sample with a hemolysate. Stability was determined by testing one sample at 0 and 24 h at room temperature, respectively. Results The assay was linear from 0–718 mg/dL of glucose with a slope of 1.05 and an intercept of 3.5. The recovery ranged from 103% to 111% in samples containing 23.2, 46.4, 92.7, and 159 mg/dL glucose, respectively. Both the intra-run and inter-run precisions for the nine samples with different glucose concentrations had a coefficient of variation of <5%. The samples were stable at room temperature for the study period of 24 h. No interference was observed at hemoglobin of 477 mg/dL. Conclusion Our study indicates that the glucose assay, GLUC3, on Roche Cobas c702 analyzer can be used to measure glucose in pancreatic cyst fluid samples. Our results show that glucose measurement in pancreatic cyst fluid had a good recovery and reproducible results with precision being <5%. This test may aid in the differential diagnosis of pancreatic mucinous cysts.