Prostate cancer is the most common type of cancer among men, which is mainly due to extensive use of screening tests and high total number of prostate biopsies. Verification of tumors with poorer prognosis is the primary goal of prostate cancer management. The study was aimed to determine the clinical and morphological associations and the prognostic value of the Nanog protein expression in prostate cancer of distinct Grade Groups. We used the prostate tissue specimens obtained during surgery, and the biopsy specimens, the total of 89 cases. Histological and immunohistochemical assessment was performed using antibodies to Ki-67 and Nanog. Correlations between the expression of markers and the Grade Groups were revealed using the Spearman's rank correlation coefficient, and the correlation with clinical and morphological characteristics was determined using the chi-squared test (χ2). There was a positive correlation between the expression of Ki-67 and Nanog, and the Grade Group numerical order (rs = 0.619, p < 0.001 and rs = 0.786, p < 0.001 respectively). We managed to find the relationship between the high Nanog expression and the extraprostatic extension (p = 0.041). High expression of Nanog protein in the prostate cancer cells was associated with a higher-grade adenocarcinoma and indicated a poor prognosis.