Identification of disease-associated epigenetic markers in early life might be useful for pre-emptive intervention to prevent diseases. Epigenome-wide association analyses using newborn blood spot screening cards are an anticipated field of research in Japan. Here, in this study, post-test dried blood spot (DBS) samples were anonymized, with only three attributes of gender, gestational age, and birth weight identified. We isolated DNA from DBS (n = 300) archived for more than 3 years. The median DNA yield (ng) per individual was 429 (interquartile range 300-565). In a model epigenetic analysis, we conducted a confirmative study on the known association between birth weight and hypoxia-inducible factor 3A (HIF3A) gene methylation. DNA methylation levels and cis-acting SNP genotypes (rs8102595 and rs3826795) were measured using EpiTYPER and Taqman assays, respectively. HIF3A methylation was positively associated with birth weight-for-gestational age centile (p = 0.021). While HIF3A methylation was associated with cis-genotypes (rs8102595, p = 2.08E-13; rs3826795, p = 3.63E-09), the association with birth weight centile was retained after adjusting for cis-genotypes (p = 0.029). Thus, we successfully reproduced the results reported previously by others, and demonstrated the usefulness of archived DBS in secondary use for epigenetic association analyses.