The genomic variation of the porcine PPARGC1A 5’ upstream region was identified and new DNA polymorphisms in the region are described. Among the polymorphisms, c.-2894G>A is considered to be a suitable molecular marker for the improvement of meat quality and good lean meat production based on the findings in a previous study. The aim of this study was to confirm the effects of the site of the polymorphism on phenotypic traits and to clarify the regulatory role of the PPARGC1A 5’ region. One hundred fifty-seven Berkshire pigs were used for association analysis. Fifty-eight pigs with specific genotypes were used to isolate mRNA from the longissimus dorsi muscle tissues, which were immediately collected from the carcasses 45 minutes after slaughter. The level of PPARGC1A mRNA expression in each single nucleotide polymorphism (SNP), including the c.-2894G>A, c.-2885G>T, and c.-1402A>T sites, was compared between genotypes using real-time quantitative PCR. Finally, to assess whether or not the c.-2894G>A polymorphism affects porcine PPARGC1A gene transcription, the luciferase assay was performed using a constructed 5’ regulatory region within the pGL3 basic vector. The results indicated that the expression of PPARGC1A mRNA significantly differed in the c.-2894G>A site (P < 0.05), and also that the transcription activity was significantly higher with the G allele than the A allele (P < 0.05). Moreover, the SNP had significant effects on phenotypic traits, including muscle fiber characteristics and lean meat production. The meat in the pigs with the GG genotype was leaner and had better lean meat production ability and quality than the meat from pigs with other genotypes (P < 0.05). Thus, it was shown that polymorphisms of the 5’ PPARGGC1A regulatory region regulate gene expression.