The present study aimed to evaluate the effects of breed and production system on quantity and quality of milk in goats. The data obtained from two groups of Markhoz goats reared in two different regions (MS and ME), and one group of Kurdish hairy goats distributed in one region (KE) were analyzed. Environmental factors and management system for MS and ME goats were different, but ME and KE goats were reared in similar conditions. The investigated traits were daily milk production (g/day), milk composition including the percentage of fat, protein, solids non-fat, lactose, ash and density (g/cm3), as well as fatty acid compositions (g/100 g total fatty acids). The number of 1260 samples for daily milk production and milk composition, as well as 45 samples for milk fatty acid profile, were used in the analysis. The milk and fatty acid composition were determined by Lactoscan SL60 and GCMass apparatus, respectively. The least-square means of fat, protein, lactose and density were affected by the breed-production system (P < 0.01). The effects of lactation stage on all traits were significant (P < 0.01), except for protein percentage (P > 0.05). Furthermore, the effect of age of goats on daily milk production was significant (P < 0.01). The proportion of C12, C16, CLA and C18:3 was influenced (P < 0.05) by the breed-production system. Also, the age of does and lactation stage had a significant impact on the amount of some milk fatty acids (P < 0.05).