High-throughput RNA sequencing (RNA-Seq) overcomes the limitations of the current hybridization-based techniques to detect the actual pool of RNA transcripts in spermatozoa. The application of this technology in livestock can speed the discovery of potential predictors of male fertility. As a first step to identify novel gene products of fertility importance in pigs, we conducted a RNA-sequence analysis of boar spermatozoa. Fresh semen of 8 fertile boars (3 ejaculates/boar) were purchased from a commercial stud and pure motile spermatozoa were obtained through a discontinuous percoll gradient. Total sperm RNA were extracted using commercial kits with an in-column DNase digestion. The purity and integrity of RNA samples were checked and those with high quality parameters were used for deep-RNA sequencing to produce millions of short cDNA reads using Illumina RNA-Seq technology. Resulting reads were aligned to the pig reference genome to produce a genome-scale transcription map that consisted of both the transcript structure and the expression level of each gene (fragments per kilobase of exon per million fragments mapped). Total of 18,357 sequence tags were successfully mapped to all pig chromosomes and mitochondrial genome. Five chromosomes (2, 1, 6, 7, and 13) comprised the highest density of mapped transcripts (42%), while the bottom lowest density (8%) was found in chromosomes 10, 18, 16, 11, and Y. The Y chromosome and mitochondrial genome contained only 0.07% and 0.08% of total mapped sequence tags. Structural annotation revealed a diverse population of sperm transcripts comprising both coding and non-coding RNAs. Approximately 12,355 of sequence tags were annotated with ENSEMBL and rRNAs (e.g., 5s and 7sk), snRNA (e.g., U1 and U6), miRNAs (e.g., mir127 and mir935), and mitochondrial RNA (e.g., ND6 and CO1) constituted the most abundant sequence tags. We further confirmed the presence of selected genes (e.g., AQP11 and AQN-1) through RT-PCR. The findings revealed a large pool of coding and non-coding RNA in mature boar spermatozoa. The full investigation of this RNA population will allow for the identification of those having critical roles during fertilization and early embryogenesis.