The study sought to determine the reliability of Heamatoxylin and Eosin (H&E) and Best’s carmine methods for the detection of glycogen in paraffin wax embedded tissues sections. This was a retrospective laboratory based study. Tissue blocks of adenocarcinoma of the ovary were retrospectively retrieved, sectioned and stained using H&E and Best’s carmine as test methods and periodic acid-Schiff (PAS) as “gold standard”. Out of 200 tissues sampled, 60.5% were PAS positive.. Based on the performance of “gold standard” (PAS), Best’s carmine and H&E had sensitivities of (88.5%; 56%) and specificities of (69.9%; 44%) respectively. Best’s carmine had positive and negative predictive values of (69.4%; 88.8%) respectively, while H&E had positive and negative predictive values of (45.5%; 54.6%) respectively. Best’s carmine had diagnostic accuracy of 78.6% and H&E 49.5%. Best’s carmine had Cohen’s kappa of 0.6 while H&E had 0.001. PAS had turn- around time (TAT) of 858 minutes, costing USD 1.17 per test, while Best’s carmine TAT of 107 minutes costing USD 1.65 per test. H&E had TAT of 65 minutes costing USD 1.21 USD per test. Exchange rate of 1 USD = Ug. Shs 2509..Best’s carmine had fairly high reliability, high TAT and fairly costly. H&E had low reliability, low TAT and fairly cheaper. PAS had highest reliability and highest TAT and very cheap. Although Best’s carmine had high TAT and fairly expensive, it would be the most preferred method in the absence of PAS.