Background: The objective of this study was to examine the risks for short-term (<= 3 months) and long-term (>3 months) chemotherapy-associated toxicities in a large population-based cohort of patients with non-small cell lung cancer from 1991 to 2002. Methods: The population consisted of 41,361 men and 30,804 women >= 65 years identified from the Surveillance, Epidemiology, and End Results-Medicare-linked database. The incidence of 50 toxicity-associated end points was calculated for 14 chemotherapy agents. Short- and long-term toxicities with a >= 2-fold increase in incidence compared with the no-chemotherapy group were defined as chemotherapy-associated toxicities. Hazard ratios and 95% confidence intervals for the risk of toxicity were calculated for the four most common chemotherapy agents for non-small cell lung cancer: cisplatin/carboplatin, paclitaxel, vinorelbine/vinblastine, and gemcitabine. Results: The most common short-term toxicities (9.2-60%) included acute anemia, nausea, and neutropenia. The most common long-term toxicities (15-37%) included acute anemia, respiratory failure, pulmonary fibrosis, dehydration, neutropenia, nausea, and fever. Multivariate analysis for selected chemotherapies demonstrated that after adjusting for other risk factors and confounders, some short-term toxicities became nonsignificant; however, almost all long-term toxicities remained significant. Long-term toxicity increased over time and was more likely in women, minority populations, those with fewer baseline comorbidities, and across disease stages. Conclusions: The administration of various chemotherapy agents for non-small cell lung was associated with a number of short- and long-term toxicities. The projected survival benefits of chemotherapy must be weighed against the risk of long-term toxicities.