Abstract Background The pathophysiology of brain injury following aneurysmal subarachnoid haemorrhage (SAH) is associated with numerous mediators. The aim of the study is to analyse protein changes after SAH in cerebrospinal fluid (CSF) using mass spectrometry (MS). Methods CSF samples were obtained from forty-four control subjects, seven good outcome and ten poor outcome SAH patients. CSF samples were collected at specific time intervals after SAH (days 1, 5 and 10). MALDI-TOF (Matrix Assisted Laser Desorption/Ionization Time-of-Flight) and ClinProTools software were utilised for MS, MS/MS (Mass Spectrometry) spectra collection and analysis. Selected masses were identified. The MALDI-TOF profiling experiments allowed for the targeted selection of potential markers in SAH. The study was performed in three steps by comparison of CSF samples: (1) from the control group and SAH patients (both good and poor outcome groups); (2) collected on days 1, 5 and 10 within the groups of poor SAH and good SAH patients, respectively; (3) from poor outcome SAH and good outcome patients at days 1, 5 and 10. Results 15 new proteins whose CSF level is alternated by SAH presence, SAH treatment outcome and time passed since aneurysm rupture were identified. Conclusions We demonstrated new proteins which might play a role in different stages of subarachnoid haemorrhage and could be a new target for further investigation.