Sigmoid sinus thrombosis (SST) usually follows acute as well as chronic otitis media with coalescent mastoiditis. A singular case of noncoalescent mastoiditis complicated with thrombosis of deep cerebral sinuses occurring in a young child is presented. A genetic thrombophilic disorder (prothrombin G20210A allele mutation) was identified as the predisposing factor for this unusual complication. Particular emphasis is placed on the course of the disease, which showed regression only after surgical exploration and additional anticoagulant therapy. We conclude that a thorough and early assessment of coagulation factors should always be performed, especially in the population at risk, in order to rule out unusual aetiologies of these rare but still life-threatening pathological processes.