Like most chemotherapy drugs, cyclophosphamide can cause a range of side effects. Common side effects include nausea, vomiting, hair loss, and fatigue. It can also cause more serious effects such as low blood cell counts, which increases the risk of infections, bleeding, and anemia. Long-term use can lead to bladder problems, including hemorrhagic cystitis, and an increased risk of secondary cancers. Patients are often monitored closely to manage these side effects.