We report the case of a two-month-old immunocompetent girl affected by Staphylococcus aureus sepsis complicated with pneumonia and pleural effusion, spondylodiscitis and endophthalmitis treated with linezolid. She developed a S. aureus sepsis in the neonatal period antibiotically treated with clinical resolution. Ten days after therapy discontinuation, the infant experienced a new S. aureus sepsis complicated by pneumonia with pleural effusion. Due to the presence of dorsal swelling, a pulmonary computer tomography was performed that showed a dorsal D5-D6 spondylodiscitis. Since the sepsis was scarcely responsive to several appropriate antibiotics, we finally decided to treat the patient with linezolid. A few weeks after changing antibiotics, the child underwent an ophthalmologic visit. Due to the finding of ocular lesions, imaging examinations were performed. The diagnosis was compatible with retinoblastoma, such that the eye was enucleated. Nevertheless, histological and microbiological investigations did not confirm the tumour hypothesis, but revealed a S. aureus abscess with retinal detachment. The child completed antibiotic therapy with linezolid and was visited periodically at the Infectious Disease Unit for a follow-up. She underwent progressive resolution of discitis and did not present any further flare of sepsis. Nevertheless, she still has a replacement device in her right eye and a D5-D6 severe kyphosis with spinal fusion.