Intratumor heterogeneity (ITH) may foster tumor adaptation and compromise the efficacy of personalized medicines approaches. The scale of heterogeneity within a tumor (intratumor heterogeneity) relative to genetic differences between tumors (intertumor heterogeneity) is unknown. To address this, we obtained 48 biopsies from eight stage III and IV clear cell renal cell carcinomas (ccRCC) and used DNA copy-number analyses to compare biopsies from the same tumor with 440 singletumor biopsies from The Cancer Genome Atlas (TCGA). Unsupervised hierarchical clustering of TCGA and multi-region ccRCC samples revealed segregation of samples from the same tumor into unrelated clusters. 25% of multi-region samples appeared more similar to unrelated samples than to any other sample originating from the same tumor. We find that the majority of recurrent DNA copy number driver aberrations in single biopsies are not present ubiquitously in late stage ccRCC and are likely to represent subclonal events acquired during tumor progression. Such heterogeneous subclonal genetic alterations within individual tumors may impair the identification of robust ccRCC molecular subtypes classified by distinct copy number alterations and clinical outcomes. The co-existence of distinct subclonal copy number events in different regions of individual tumors reflects the diversification of individual ccRCCs through multiple evolutionary routes and may contribute to tumor sampling bias and impact upon tumor progression and clinical outcome.