Superficially invasive (pT1) papillary urothelial cell carcinomas (UCCs) may run a variable course. Several attempts have been made for the substaging of UCC to identify the clinically aggressive tumors. We present a new substaging system, based on the extent of invasion. From a series of 53 primary pT1 UCC, 24 cases showed invasion of the subepithelial stroma by an invasive front extending more than a maximum length of 0.5 mm (pT1mic), and 29 showed extensively (>0.5 mm) infiltrating UCC (pT1ext). We tested diagnostic reproducibility between 2 pathologists and found 81% agreement. Furthermore, all cases were analyzed for mutations in the fibroblast growth factor receptor 3 (FGFR3) gene, which represents the favorable pathway of urothelial cell carcinogenesis. Mutant FGFR3 was commonly observed in pT1mic UCC (15/24, 63%), but rarely (2/29, 7%) in pT1ext UCC (chi2 test, P < .001). The presence of pT1ext at initial diagnosis proved to be the strongest predictor for progression, also when adjusted for FGFR3 mutation status in a Cox regression model. If confirmed on a larger series of pT1 UCC, this relatively simple and new substaging system for pT1 UCC may prove to be of prognostic value and supportive to clinical decision-making.