Background: Factors that stratify the risk of Gastrointestinal stromal tumors (GISTs) include mitotic rate, tumor size and location. However, mitotic counting is subjective and time-consuming. We focused to identify value of recently reported mitotic marker, anti phophohistone H3 (PHH3) in GISTs. Methods: Between 2012 and 2013, 77 cases of primary GIST were reviewed for mitotic count (/50HPFs) and immunohistochemical staining for Ki-67 and PHH3 was performed. Ki-67 labeling index (LI) was measured by the proportion (%) of the total positive cells. The numbers of PHH3 positive nuclei were calculated per 50 HPFs for PHH3 mitotic index (MI). Statistical analyses were carried out using Spearman’s rank correlation for comparisons among mitosis, Ki-67 and PHH3. Interobserver agreement of measuring mitosis and PHH3 MI was calculated by interclass correlation coefficients. Results: The tumor sites included stomach (n=54), duodenum (n=12), ileum/jejunum (n=10) and rectum (n=1). Mean tumor size was 4.98cm (range, 1-36cm). Mitotic counts ranged from 0 to 138 per 50 HPFs (mean 24.0). Ki-67 LI ranged from 1% to 25% (mean 9.04). PHH3 MI ranged from 0 to 126 per 50 HPFs (mean 26.3). After adjusting PHH3 MI, risk of GISTs changed in 9 cases. A positive correlation was found in mitotic counts and PHH3 MI (Spearman rank correlation, r = 0.810, p<0.001) and Ki-67 LI (Spearman rank correlation, r = 0.605, p<0.001). Interobserver correlation coefficient was 0.975 [confidence interval (CI) = 0.962-0.983] for 3 observers in measuring mitotic counts and 0.940 [confidence interval (CI) = 0.912-0.961] in measuring PHH3 MI. Conclusions: PHH3 MI correlated very well with mitotic counts and can be used as an useful adjunctive to count mitotic index more efficiently in GISTs.