Venous thromboembolism may involve venous sites other than the lower limbs, such as cerebral, splanchnic, and upper limb veins. Although uncommon, these thromboses may be clinically severe and challenging for caregivers. In this review, the main pathogenic, clinical, and therapeutic features of thromboses in rare venous sites are discussed. Even though there was a lot of recent progress in understanding the mechanistic role of inherited and acquired thrombophilia and of the interactions between different risk factors, the optimal management of these patients is still unsettled, being currently based on the consensus of experts due to the lack of randomized trials. The implementation of large interdisciplinary registries is a necessary weapon to optimize the treatment of rare venous diseases.