OBJECTIVES: The aim of this study was to assess the quality of histological slides deparaffinized with xylene and commercial alternatives to xylene and to compare the quality of slides of human brain deparaffinized using these methods. STUDY DESIGN: Cross-sectional study. MATERIAL AND METHODS: The study was conducted on tissue samples from the Clinical Institute of Pathology and Forensic medicine, University Hospital Osijek. Ten samples of nervous tissue were embedded in paraffin and cut on a microtome into 6 µm sections. Each sample was cut into 6 sections. The sections were divided into three groups of 20 sections: one group was deparaffinized with xylene, the second group was deparaffinized with Tissue-Tek Tissue-Clear, and the third group was deparaffinized with Citrosol. One half of all sections was stained with hematoxylin-eosin stain, and the other half was stained using the Kluver-Barrera staining method. The quality of slides was evaluated by three histologists and the following parameters were evaluated: nuclear staining, cytoplasm staining, staining crispness, uniformity of the staining and method-related artifacts. RESULTS: Hematoxylin-eosin stained nervous tissue slides showed no statistically significant difference in quality, regardless of the method of deparaffinization. However, slides stained using the Kluver-Barrera method and deparaffinized with Tissue-Tek Tissue-Clear provided significantly poorer results regarding crispness and uniformity of staining compared to the slides deparaffinized with xylene and Citrosol. Despite that, both Tissue-Tek Tissue-Clear and Citrosol proved to be sufficiently efficient to replace xylene. CONCLUSION: When it comes to deparaffinization, Citrosol proved to be as efficient as xylene. Tissue-Tek Tissue-Clear provided somewhat poorer results than Citrosol and xylene; however, all three methods provided are sufficient quality for use in both diagnostics and scientific research.