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Background Microsatellite instability (MSI) occurs in several cancer types and is commonly used for prognosis and as a predictive biomarker for immune checkpoint therapy. Methods We analyzed n = 263 formalin‐fixed paraffin‐embedded (FFPE) tumor specimens (127 colorectal cancer (CRC), 55 endometrial cancer (EC), 33 stomach adenocarcinoma (STAD), and 48 solid tumor specimens of other tumor types) with a capillary electrophoresis based multiplex monomorphic marker MSI‐PCR panel and an amplicon‐based NGS assay for microsatellite instability (MSI+). In total, n = 103 (39.2%) cases with a known defect of the DNA mismatch repair system (dMMR), determined by a loss in protein expression of MSH2/MSH6 (n = 48, 46.6%) or MLH1/PMS2 (n = 55, 53.4%), were selected. Cases with an isolated loss of MSH6 or PMS2 were excluded. Results The overall sensitivity and specificity of the NGS assay in comparison with the MSI‐PCR were 92.2% and 98.8%. With CRC cases a nearly optimal concordance was reached (sensitivity 98.1% and specificity 100.0%). Whereas EC cases only show a sensitivity of 88.6% and a specificity of 95.2%, caused by several cases with instability in less than five monomorphic markers, which could be difficult to analyze by NGS (subtle MSI+ phenotype). Conclusions MSI analysis of FFPE DNA by NGS is feasible and the results show a high concordance in comparison with the monomorphic marker MSI‐PCR. However, cases with a subtle MSI+ phenotype, most frequently manifest in EC, have a risk of a false‐negative result by NGS and should be preferentially analyzed by capillary electrophoresis. Microsatellite instability (MSI) analysis of formalin‐fixed paraffin‐embedded (FFPE) DNA by NGS is feasible and the results show a high concordance in comparison with the monomorphic marker MSI‐PCR (overall sensitivity and specificity of the NGS assay in comparison with the MMR‐IHC/MSI‐PCR were 92.2% and 98.8%). However, cases with a subtle MSI+ phenotype, most frequently manifest in endometrial cancer (EC), have a risk of a false‐negative result by NGS and should be preferentially analyzed by capillary electrophoresis.