Gene expression profiling of muscle-invasive bladder cancer (MIBC) could aid treatment selection for patients with this disease. Increased immune infiltration in tumours was associated with improved disease-specific survival (DSS) in patients treated with trimodality therapy. However, increased stromal infiltration was associated with reduced DSS in patients who received neoadjuvant therapy and radical cystectomy. These results suggest that the tumour microenvironment influences treatment outcomes in MIBC.