Unexplained male infertility (UMI) is a condition in which routine semen analysis fails to detect subcellular sperm dysfunctions. In the present research, a comparative proteomics study of seminal plasma (SP) was conducted in men with unexplained infertility whose female partners had undergone in vitro fertilisation (IVF) treatment to find differences in the SP protein profile. Five UMI men with successful and eight with unsuccessful IVF outcome enrolled in this study. Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) technique was used for protein separation. The differentially expressed proteins were identified using mass spectrometry. Results indicated that at least two different protein spots, including clusterin and epididymal secretory protein E1, were over-expressed (1.5- and 2-fold change, respectively, p<0.05) while prostate-specific antigen was downregulated (0.3-fold change, p<0.05) in the successful group as compared with the unsuccessful group. Considering the role of all three identified proteins in the sperm quality, the results of the present study introduced these proteins as new candidate biomarkers for success of IVF in UMI couples.