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This study was conducted to evaluate effects of breed, parity, sampling day, and sampling time on somatic cell count (SCC) and milk lipid and protein profiles in intra-mammary infection-free early lactating dairy cows (Holstein, n = 5 and Swiss Brown, n = 6; 34 ± 6 DIM). SCC was assessed by flow cytometry. Milk lipid (free fatty acid, triacylglycerol, diacylglycerol, cholesterol, phospholipid) and protein IgG and A, albumin, caseins (α, β, κ), α-lactalbumin, and β-lactoglobulin were determined using HPTLC and SDS-PAGE methods. Data were analysed by 4-way ANOVA and subjected to hierarchical backward elimination of insignificant interaction terms. SCC varied by parity and sampling time. Apart from sampling time, other fixed factors altered milk lipids. There was only a breed x parity interaction effect on milk lipid profiles. All proposed factors affected milk proteins. Among proteins only the IgG fraction exhibited diurnal variation. There were significant breed x parity, breed x sampling day, and parity x sampling day interactions for milk proteins. In conclusion, factors relating to the cows themselves (breed and parity), sampling day, and sampling time cause variation in parameters that are pertinent to mammary gland health and milk quality. [ABSTRACT FROM AUTHOR]