Using Surveillance, Epidemiology and End Results (SEER)-Medicare data (1996-2010), we compared survival and toxicity outcomes in 6993 patients older than 65 years with follicular (FL), nodal marginal zone (NMZL) and small lymphocytic lymphoma (SLL) receiving front-line therapy with rituximab (R), RCHOP (R, cyclophosphamide, doxorubicin, vincristine, prednisone), RCVP (R, cyclophosphamide, vincristine, prednisone) or R-fludarabine-containing regimens within 3 years from diagnosis. We demonstrated significant heterogeneity by histology after various regimens in multivariable survival models. Compared with RCHOP, overall survival was inferior with fludarabine-based regimens in FL (hazard ratio [HR] 1.53, p = 0.0001) and NMZL (HR 1.88, p = 0.0018). Conversely, in SLL outcomes were similar with any regimen. In NMZL and SLL, survival was not significantly different after single-agent R compared with multi-agent combinations. Choice of front-line chemotherapy may thus impact survival in older patients with indolent lymphomas, and heterogeneity by histology should be accounted for in clinical trials.