Micronutrients are important co-factors or substrates to enzymes that protect and repair DNA against damage or methylation. Micronutrient deficiency could induce genomic instability and changes in DNA leading to cell apoptosis and degenerative diseases. The objective of this study was to compare the sperm transcriptome of boars receiving a diet supplemented with high amounts of methylating micronutrients (methionine, choline, betaine, vitamin B6, folate, and vitamin B12) relative to boars with non-supplemented diet. Semen mRNA from 4 boars was profiled and single-end reads were mapped to the Sus scrofa reference genome (UCSC susScr3) using Tophat v2.012. In total, 477 transcripts from 446 genes were tested and 73 transcripts from 72 genes were differentially expressed between the supplemented and non-supplemented boars using Cufflink v2.2.1 (P-value <0.05). Among the differentially expressed transcripts, 89% of those from boars with the supplemented diet were overexpressed relative to those from non-supplemented boars. The porcine seminal protein II (PSP-II) was under-expressed; meanwhile, the AWN protein (AWN) was overexpressed in boars with the supplemented diet relative to non-supplemented. PSP-II encodes a protein with paradoxical functions: in vitro PSP-II enhances viability, motility and mitochondrial activity of highly-extended boar spermatozoa; in vivo PSP-II triggers the recruitment of polymorphonuclear leukocytes and T cells in the uterus of the sow after mating. AWN encodes a sperm surface-associated protein that participates in sperm adhesion to the egg. Functional analysis of the differentially expressed genes using DAVID identified one category cluster (enrichment score >6) related to cellular metabolism and biosynthetic process, structural constituents of ribosomes and structural molecular activity. The limited differentially expressed transcripts and the solely functional category enrichment suggest that methylating micronutrients in high quantities had no impact on the transcriptome of sperm cells.