Recurrent pregnancy loss affects approximately 3–5% of couples attempting to have a child. It is defined as the occurrence of two or more consecutive pregnancy failures before 20 weeks of gestation. In about 40% of cases, the cause remains unknown and are defined as idiopathic recurrent miscarriages (iRM) (Stephenson and Kutteh 2007). However, most of these diagnostics tests are performed in the female partner, with the male’s contribution remaining relatively underexplored (only paternal karyotyping is done). Paternal factor may be the underlying aetiology in RM (Lalancette et al. 2008) and molecular abnormalities in sperm may have an adverse effect on embryonic development. Certain portion of sperm genome remains transcriptionally active and codes for transcripts which are of paramount developmental importance (Krawetz 2005; Gil-Villa et al. 2010). Among these, the role of long-lived sperm RNA which are not translated is controversial. Sperm possess a remarkable set of long-lived messenger RNAs (mRNAs) that have been hypothesized to be required for embryogenesis. Some of these spermatozoal mRNAs are also found in zygote, indicating that these transcripts may be functionally critical during embryonic development (Ostermeier et al. 2004). The delivery of certain sperm transcripts to the oocyte, which could translate to proteins, may be critical for the early stages of embryogenesis and/or implantation. In the vast population of mRNA, transcripts of winglesstype MMTV integration site family, member 5A (WNT5A), heat shock protein 90 (HSP90) and protamine 2 (PRM2) are present in human mature spermatozoa as examined by microarray and serial analysis gene expression (SAGE) technology (Wykes et al. 2000; Zhao et al. 2006). These genes