Idiopathic partial thrombosis of the corpus cavernosum (IPT) is a rare cause of perineal pain involving thrombosis within the proximal corpora cavernosa. This article clarifies the aetiology and makes recommendations on diagnosis and treatment. Three cases are described and a systematic review of the literature is presented. Magnetic resonance imaging (MRI) scans of the penis conducted for reasons other than IPT were also reviewed, to compare the normal anatomy of the corpora cavernosa with that of IPT patients.Twenty-nine IPT cases were identified, including the three described here. All patients presented with perineal pain and in all cases the thrombus was located in the proximal part of the corpora cavernosa.IPT has been associated with haematological diseases, drugs, prior priapism, sexual activity, bicycle riding and aeroplane flights. A fibrous septum within the corporeal tissue has been identified with advanced imaging modalities. Ultrasound, computed tomography and MRI have proven useful in the diagnosis. Both surgical and medical treatments have been attempted and the results have usually been good. However, two cases of surgical treatment have resulted in erectile dysfunction. It is suggested that ITP is based on the development of penile thrombosis and/or priapism in the presence of a pre-existing fibrous septum in the corpora cavernosa. MRI should be used to confirm the presence of a thrombus and a septum. First choice of treatment is pain medication and systemic anticoagulation; more invasive treatments should only be attempted only if this approach fails.