Overexpression of mitotic arrest deficient 2 (MAD2) and/or cell division cycle 20 (CDC20) in the spindle assembly checkpoint leads to chromosomal instability and aneuploidy. Cell-in-cell (CIC) structures are formed by the process where cancer or immune cells are internalized into adjacent host cancer cells. Here, we investigated the clinicopathological significances of spindle assembly checkpoint protein overexpression and CIC structures in 829 cases of normal, premalignant, and gastric cancer (GC) lesions. MAD2 and CDC20 expressions were significantly increased in intestinal metaplasia, low-grade dysplasia, high-grade dysplasia (HGD), and early GC than normal mucosa, and their expression levels were the highest in HGD. Interestingly, CDC20 immunohistochemistry specifically stained the outer cells of CIC structures, which were the most frequently observed in early GC. In univariate analyses, MAD2 and CDC20 overexpressions and CIC formation were associated with older age, intestinal histology, lower tumor-node-metastasis stage, and longer recurrence-free survival and cancer-specific survival of GC patients. In multivariate survival analyses, MAD2 and CDC20 overexpressions were associated with better recurrence-free survival (hazard ratio, 0.61; P = .012) and cancer-specific survival (hazard ratio, 0.63; P = .043), respectively. In conclusion, MAD2 and CDC20 are the most expressed in HGD, suggesting their roles in the early stage of gastric carcinogenesis, whereas their overexpressions in GC are associated with intestinal histology and favorable clinicopathological parameters, which may be useful for immunohistochemical classification of chromosomal instability-type GC. Moreover, CDC20 is a novel immunohistochemical marker for highlighting CIC structures.