To study the toxicities associated with pulse cyclophosphamide therapy and to compare then with patients without cyclophosphamide exposure. In this retrospective cross-sectional observational study Systemic Lupus Erythematosus (SLE) patients who had received immunosuppressive agents in the past were interviewed in the out patient department for drug related toxicities. Patients were asked about the any history of tuberculosis, herpes zoster, hemorrhagic cystitis or ovarian toxicity in the past. Among 90 patients 84 (93%) were females. The mean age at the start of therapy was 29-7+9-95 (range 8-67) years. Thirty-eight patients (34 females) had received cyclophosphamide. The mean cumulative dose of cyclophosphamide was 9.2+4.2 (range 1-20) grams and mean time duration from start of cyclophosphamide exposure to enrollment was 3.6+3.2 (range 0.4-11) years. Of the rest 52 (50 females) patients 30 had received only steroids, 18 had received only azathioprine and 4 patients had received only hydroxychloroquine. There was a higher occurrence of transient amenorrhea (10/34 versus 2/50, p0.001) and premature menopause (6/34 versus 1/50 p 0.02) in patients treated with cyclophosphamide as compared to those who had not received it. Patients with cyclophosphamide exposure had higher prevalence of Hematuria (2 versus 0 patients), tuberculosis (4 versus 1 patient) and herpes zoster infection (3 versus 0 patients) but these differences were not significant statistically. Transient amenorrhea was seen in one-third and premature menopause was seen in onesixth of LCE with cyclophosphamide exposure.