Microsatellite instability (MSI) characterizes a special molecular genetic subtype of malignancies and is associated with the deficiency of mismatched DNA repair. There are no reliable data on the frequency of MSI in colorectal neuroendocrine neoplasms due to the relative rarity of this cancer type. The prognostic significance of MSI is debatable. The aim of this study was to investigate the frequency of the MSI phenotype among colorectal neuroendocrine neoplasms (NENs) with different primary location, grade and stage. Twenty-nine patients (15 men and 14 women, mean age: 62.5 years) included in the study underwent surgery for colorectal neuroendocrine tumors between 2015 and 2018. The mean follow-up period was 3.8 years.  Colorectal NENs were grouped by primary location and stage. The majority of the patients (52%) had stage III cancer at diagnosis. The microsatellite stability (MSS) phenotype was confirmed in 24 patients (83%), whereas the MSI phenotype was observed in 5 patients (17%). All MSI-positive tumors were stage I well-differentiated grade G1 or G2 neuroendocrine tumors (NETs) of the rectum. Overall survival was 50% for patients with stage II MSS-positive NENs of the colon and rectum, 33% for stage III and 0% for stage IV. For patients with stage I MSI-positive NENs of the rectum, overall survival was 100%. Thus, the frequency of MSI-positive colorectal NENs was estimated.