This study aimed to identify the expression levels of some candidate genes for mastitis resistance (LTF and BRCA1), milk yield (POU1F1 and IGF-1), and milk quality (PPAR gamma and CSN2) in different feeding systems (pen- and pasture-based) used for Damascus goats. Milk samples were taken from all goats in both pen and pasture groups at 4 times, at the 1st, 3rd, 5th, and 7th months of the study. It was found that, compared to the pen group, the LTF and CSN2 genes in the pasture group had significant levels of upregulation in the 7th month of lactation (3.538- and 5.436-fold, respectively), the PPAR gamma gene had downregulation at the beginning of lactation (0.399-fold), and the IGF-1 gene had upregulation in the 3rd month of lactation (2.313-fold) but had significant levels of downregulation (2.332-fold) in the 5th month of lactation. It was determined that LTF gene expression levels in goats might be used as a criterion in identifying mastitis resistance, IGF-1 for lactation milk yield, and PPAR gamma for milk fat yield. This study is the first report that presents LTF, BRCA1, IGF-1, and PPAR gamma gene expression levels in goat milk and udder epithelial cells and the effect of BRCA1, POU1F1, and PPAR gamma genes on milk protein yield.