As part of a population health assessment of goats, a cross-sectional study with 356 goats (n=178 Alpine and 178 Saanen) was performed. A comparison was made between biochemical markers, hematological profile, composition of milk, somatic cell count, and milk fatty acid profile in Alpine and Saanen goats. The highest concentration of non-esterified fatty acids, triglycerides, urea, and alkaline phosphatase was found in Alpine goats. The lowest concentration of sodium ion and chloride ion was observed in Saanen goats. The concentration of glucose, total cholesterol, β-hydroxybutyrate, albumin, globulin, total protein, calcium ion, inorganic phosphate, potassium ion, magnesium ion, and γ-glutamyl transferase showed no breed difference. The red blood cell count, hematocrit, hemoglobin, mean cell volume, mean cell hemoglobin, mean cell hemoglobin concentration, white blood cell count, neutrophils, lymphocytes, monocytes, eosinophils, basophils, platelet count, and mean platelet volume showed no breed difference. Milk yield indicated that Saanen goats produced more milk. However, their milk fat and milk protein were lower compared to Alpine goats. Non-fat solids, density, cryometry, and pH showed no breed difference. The somatic cell count was higher in Alpine goats. The highest concentration of fatty acids was for palmitic and oleic. The highest concentration of butyric was observed in Saanen goats. However, their caprylic, capric, lauric, and myristic content was lower compared to those shown by Alpine goats. The concentration of caproic, myristoleic, palmitic, palmitelaidic, palmitoleic, stearic, elaidic, oleic, linolelaidic, linoleic, arachidonic, and behenic acids showed no breed difference. The results obtained can be used as reference values and influence the price paid by the Mexican goat dairy industry.