The safety profile of lenalidomide use in lower-risk myelodysplastic syndromes (MDS) patients with del(5q) is well-established, but less is known in non-del(5q) patients. We provide safety data from a randomized, phase 3 trial evaluating lenalidomide in 239 patients with lower-risk non-del(5q) MDS ineligible/refractory to erythropoiesis-stimulating agents (ESAs). Compared with placebo, lenalidomide was associated with a higher incidence of grade 3–4 treatment-emergent adverse events (TEAEs; 86% vs. 44%), but not risk of infection (p =.817) or hemorrhagic events (p = 1.000). Grade 3–4 non-hematologic TEAEs were rare (the incidence of grade 3–4 pneumonia, e.g. was 5.6% in the lenalidomide group and 2.5% in the placebo group). Common grade 1–2 non-hematologic TEAEs did not require dose modifications or treatment discontinuation. Acute myeloid leukemia and second primary malignancies incidence was similar across treatment groups. Lenalidomide had a predictable and manageable safety profile in lower-risk non-del(5q) MDS patients ineligible/refractory to ESAs. Guidance on managing lenalidomide-related TEAEs is provided to help maintain patients on therapy to achieve maximum clinical benefit. TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT01029262.