Clinical outcomes in ANCA-associated vasculitis (AAV) and lupus nephritis have improved greatly with treatment regimens containing high-dose glucocorticoids and cyclophosphamide. However, with the use of these medications come significant adverse events, most notably infections, cytopenias, malignancies, and reproductive abnormalities. Multiple recent randomized controlled trials in AAV and lupus nephritis have compared cyclophosphamide-based regimens with agents such as rituximab, mycophenolate mofetil, and azathioprine, with the hope of providing better clinical outcomes with improved safety profiles. Although some of these newer regimens are now considered first-line treatments of these diseases, their adverse event profiles have been disappointingly similar to those of cyclophosphamide-based protocols. Physicians and patients should consider the adverse event profiles generated by these trials in the context of their extensive use in other patient populations, as well as available measures to prevent such events, when choosing the ideal regimen for an individual patient.