We describe three cases of split median raphe of the penis (SMR) from our hospital newborn records from 2004 to 2013. One case was associated with median raphe cyst, one with skin hypochromia, and one with a scar-like aspect of the region of interest. SMR is thought to be the result of defective fusion of ectodermal tissue in the urethra and scrotum area or of defective growth of the perineal mesoderm around the urethra during gestation. Although SMR associated with other major penile congenital defects (epispadias, hypospadias, penile torsion, bifid scrotum, chordee) is common, isolated SMR is probably an underdiagnosed (although not rare) malformative condition. Recognizing SMR in a newborn may be of educational value to neonatologists because it leads to the search for and exclusion of the above-mentioned pathologic conditions.