The objective of this study was to evaluate long-term clinical and radiological outcomes in children treated with lateral sinus thrombosis secondary to acute mastoiditis considering also contralateral sinus hypoplasia. This study was a retrospective chart review, conducted in tertiary pediatric hospital. Medical reports of eight children with acute mastoiditis and lateral sinus thrombosis from 1998 to 2011 were examined in terms of therapy, clinical recovery and radiological proof of lateral sinus recanalization. Three children presented hypoplasia of contralateral venous drainage system. Condition of sinuses was regularly monitored with MRI. Otologically and neurologically, all children recovered fully. All received antibiotics; six received additional low molecular weight heparin therapy. Mastoidectomy was performed on six cases. Incision and thrombectomy were applied in the other two, one involving internal jugular vein ligation. This latter case presented also contralateral venous hypoplasia; visual impairment proved permanent. The other two children with contralateral sinus hypoplasia recovered fully after steroid, dehydration and low molecular weight heparin therapy. Recanalization occurred in all children except the one with internal jugular vein ligation, in whom good collateral circulation was observed. There were no bleeding complications. Anatomical variations of cerebral venous drainage system can frequently be observed and should be considered in treatment planning. Mastoidectomy with antibiotics and additional low molecular weight heparin treatment is a safe, promising alternative to thrombectomy and internal jugular vein ligation in children with lateral sinus thrombosis following acute mastoiditis, also having contralateral sinus hypoplasia. Recanalization can be expected within two to five months.