Aim: Assessment of KIT and PDGFRA mutations frequencies in a Portuguese series of gastrointestinal stromal tumours (GISTs). Methods and Results: Seventy-eight GISTs were evaluated for CD117 expression and screened for mutations in KIT (exons 9, 11, 13, 14 and 17), and PDGFRA (exons 12, 14 and 18) genes. KIT activating mutations were identified in 44 (56%) of the 78 GISTs. Forty cases (91%) presented a mutation in KIT exon 11 and 4 (9%) in exon 9. One case showed a 4 bp deletion in intron 14. PDGFRA mutations were observed in cases 5 (6%), 2 (3%) in exon 12 and 3 (4%) in exon 18. Survival analysis was performed in 63 of the 78 GISTs. The presence of mutated KIT was significantly correlated with shorter survival of patients (P=0.0460), and inversely associated with epithelioid histological type of GISTs (P=0.0064). Conclusions: Overall, the incidence of both KIT and PDGFRA mutations in these Portuguese series was 63%, being in agreement with other studies, mainly of Iberian populations. The great majority of mutations were located in KIT exon 11, statistically associated with worse prognosis and indicative of favourable response to Imatinib-based therapy in this Portuguese series of GISTs.