To evaluate acute and late toxicities in patients of chordoma treated with hypofractionated, image guided pencil beam scanning proton beam therapy.Consecutive patients diagnosed with spinal chordomas treated at our center with pencil beam scanning proton beam therapy (part of a prospective SCCORE- Sarcoma, Chordoma, Chondrosarcoma registry) were included in this study. Among all patients, high risk CTV (CTV-HR) was treated to a dose of 70.4CGE/32fractions and intermediate risk CTV (CTV-IR) was treated to a dose of 57.6-64CGE/32fractions. Patients underwent clinical, radiological (including metabolic- DCE MRI imaging) and QOL (EORTC QOL QC-30) evaluations at baseline and 6 monthly thereafter. Acute and late toxicities were recorded at each clinical visit as per CTCAE V4.0 and LENT SOMA scales respectively. Clinical and radiological outcomes are being reported in this study.Consecutive 23 patients with a median age of 38 years (range 4-64 years) with histologically proven chordoma (20 classical chordomas, 1 chondroid chordomas and 2 de-differentiated chordomas were analyzed. Among patients with skull base and dorsal chordomas (15 patients) all patients underwent surgery at least once, 21% underwent surgery twice, 14% underwent thrice and 7% underwent more than 3 times. Among patients with sacral chordomas (8 patients), 63% underwent surgery at least once and 50% underwent more than once. 17% patients (2 clival and 2 sacral) underwent prior radiation with photons (IMRT technique) with 13% receiving more than once. Mean volumes of CTV HR and for skull base chordomas was 32.4cc (0.83-132cc) and for sacral chordomas was 855cc (96.1-1740cc). Two patients had acute grade 3 dermatitis, 1 patient had acute grade 3 oropharyngeal mucositis and 1 patient had acute grade 3 gastrointestinal mucositis. 28.5% of patients with Clival and 50% of patients with Sacral lesions had grade 2 acute toxicities. 1 patient had late grade 3 toxicity requiring tracheostomy. None of patients had any late grade 2/3 gastrointestinal or genitourinary toxicities. With a median follow up of 17 months (9-23 months), 21 patients (91%) remained radiologically stable with favorable metabolic response in all the 10 patients (43%) where metabolic imaging was available. Only 1 patient had in-field radiological progression and 1 patient had distant bone metastases.Pencil beam scanning proton beam therapy is feasible in patients with spinal chordomas. Despite high doses, large treatment volumes and large number of patients receiving prior treatments, the acute and late toxicities were relatively low in this cohort.