The aim of this study was to identify prognostic factors for toxicity to treatment with imatinib. The study was based on 942 patients with gastrointestinal stromal tumours (GIST) randomised to receive imatinib at different doses. The correlation between toxicities occurring with a Common Toxicity Criteria (CTC) grade 2 or more (non-haematological) or grade 3 or 4 (haematological) and imatinib dose, age, sex, performance status, original disease site, site and size of lesions at trial entry, baseline haematological and biological parameters was investigated. Anaemia was correlated with dose and baseline haemoglobin level, and neutropaenia with baseline neutrophil count and haemoglobin level. The risk of non-haematological toxicities was dose dependent and higher in females (oedema, nausea, diarrhoea), and in patients of advanced age (oedema, rash fatigue), poor performance status (fatigue and nausea), prior chemotherapy (fatigue), tumour of identified gastrointestinal origin (diarrhoea) and small lesions (rash). A multivariate risk calculator that can be used in the clinic for individual patients is proposed.