Toll-like receptors (TLRs), an important family of pattern-recognition receptors, and antimicrobial peptides (AMPs) contribute to the first line of innate protection of mammals against microbes. To compare characteristics of innate immunity between Tibetan and Yorkshire pigs, we investigated the mRNA abundance of TLR genes (TLR1-TLR9) and two AMP-encoding genes (PBD-1 and PR-39) in thymus, spleen, blood, palatine tonsils, and mesenteric and pulmonary hilar lymph nodes of the two breeds at ages of 6, 12 and 24 weeks using quantitative real-time PCR. Results showed that all mRNAs were detected in all tissues. Transcript levels of the major TLR genes of Tibetan pigs were significantly higher than those of Yorkshires in most tissues of the immune system, with a higher abundance of porcine (PBD-1) (beta-defensin-1) and PR-39 mRNA in lymphoid organs and tissues, especially blood, palatine tonsils, and mesenteric and pulmonary hilar lymph nodes. Our data suggest that Tibetan pigs have stronger innate immunity for triggering local and/or systemic immune responses to eliminate infections with pathogenic microorganisms.