Background: Blocking both gonadal and extragonadal androgens with leuprolide and abiraterone acetate (AA) is approved by the FDA to treat mCRPC. Applying this treatment in the neoadjuvant setting reduced intratumoral testosterone levels in our Phase 2 trial, but pathologic CR's were rare and minimal residual disease was observed in some patients. Methods: We performed laser capture microdissection to isolate pure foci of residual tumor cells from 19 patients who underwent RP following 24 weeks of leuprolide plus AA. We also isolated 19 foci of matched benign glands as germline controls. In 15 of the 19 cases, we dissected 2 spatially-distinct foci of residual tumor. We then performed whole exome sequencing to assess somatic mutations and copy number variations (CNVs). Results: A diversity of genomic resistance mechanisms were observed. Resistance to AA as predicted by mutation of the ligand binding domain of AR was observed in only one case. In contrast, the majority residual tumor foci harbored CNVs coinciding with gain of oncogenes or loss of tumor suppressor genes. Importantly, only a limited number of alterations were shared between foci from the same case, as most mutations were unshared. Shared CNVs frequently included arm-level single copy losses of 10q (PTEN), 13q (BRCA2), 5q (CHD1), 17p (TP53), 16q (ZFHX3) and 8p (NKX3-1), and gain of 8q (MYC). Mutations not shared by foci in the same case included further biallelic inactivation of PTEN, BRCA2 and TP53, as well as point mutations and single copy losses of BRCA1 and RB1. Distinct, focal gains included AR, PIK3CA and BRAF, and mutations also accumulated in KMT2B, KMT2C and KMT2D. Conclusions: By sampling multiple foci of residual tumor, we identified mutations that likely emerged by subclonal selection by ADT, which cooperated with the shared, clonal mutations that contributed to de novo development of the index lesion. Strikingly, the spectrum of alterations mimics mCRPC with enrichment for alterations affecting cell cycle, DNA damage repair and chromatin modifier pathways. If these alterations permit the tumor to evade AR directed therapy and subsequently mediate relapse, adjuvant therapies targeted to these mutations may increase survival. Clinical trial information: NCT00924469