Neoadjuvant chemotherapy (NAC) induces a pathologic complete response (pCR) in approximately 30% of patients with triple-negative breast cancers (TNBC). In patients lacking a pCR, NAC selects a subpopulation of chemotherapy-resistant tumor cells. To understand the molecular underpinnings driving treatment-resistant TNBCs, we performed comprehensive molecular analyses on the residual disease (RD) of 74 clinically-defined TNBCs after NAC including next-generation sequencing (NGS) on 20 matched pre-treatment biopsies. Combined NGS and digital RNA expression analysis identified diverse molecular lesions and pathway activation in drug-resistant tumor cells. Ninety percent of the tumors contained a genetic alteration potentially treatable with a currently available targeted therapy. Thus, profiling residual TNBCs after NAC identifies targetable molecular lesions in the chemotherapy-resistant component of the tumor which may mirror micro-metastases destined to recur clinically. These data can guide biomarker-driven adjuvant studies targeting these micro-metastases to improve the outcome of patients with TNBC who do not respond completely to NAC.