Few studies have examined the association between specific sources of protein and blood lipids in a national sample of adults. We examined this relationship in a sample of adults 20 years and older who participated in phase 1 (1988-91) of the Third National Health and Nutrition Examination Survey, a representative sample of the United States non-institutionalized population. After excluding those participants who reported having been told they had high blood cholesterol concentrations, the final sample size was 6228. Mean intakes of different sources of proteins, as a percentage of total protein, were compared in quartiles of blood lipids. Intakes were adjusted for age, sex and race. Additional adjustments were made for other dietary variables, recall day, BMI, smoking, and income. We observed a lower percentage meat, fish and poultry (MFP) protein intake, including a lower percentage of beef and pork protein, among persons in the lowest quartile of serum total cholesterol and apolipoprotein B (ApoB) concentrations than among persons in the higher quartiles. The percentage of plant protein intake was higher in the lowest quartile than in the highest quartile of serum cholesterol. We also observed a higher percentage of fruit protein intake with lower serum cholesterol and ApoB concentrations. We conclude that in this cross-sectional sample, consumption of MFP proteins was consistently higher among persons with higher cholesterol concentrations while consumption of plant proteins was consistently higher among persons with lower cholesterol concentrations. Our findings support the importance of assessing intake of specific protein sources, especially in studies that address dietary intake in relation to blood lipids.