Purpose Consumption of the algae spirulina (Arthrospira platensis or maxima) and wakame (Undaria pinnatifida) has been shown to lower LDL cholesterol concentrations in animals and humans, possibly due to the inhibition of intestinal cholesterol absorption. This mechanism, however, has never been investigated in humans. Therefore, we examined in nonhypercholesterolemic men and women the effects of spirulina and wakame consumption on serum markers for intestinal cholesterol absorption. Methods Thirty-five healthy men and women without hypercholesterolemia consumed in a random order daily 4.8 g spirulina, wakame or placebo for 17 days, separated by 14-day washouts. After 17 days, serum cholesterol-standardized campesterol, sitosterol and cholestanol, and lathosterol concentrations were measured as markers for intestinal cholesterol absorption and cholesterol synthesis, respectively. Concentrations of serum total cholesterol, LDL and HDL cholesterol, triacylglycerol, and plasma glucose, and blood pressure were measured as well. Results Compared with placebo, spirulina or wakame did not affect serum cholesterol-standardized campesterol (CI − 0.23 to 0.10 μmol/mmol, P = 0.435 and CI − 0.14 to 0.19 μmol/mmol, P = 0.729, respectively), sitosterol (P = 0.314 and P = 0.112), cholestanol (P = 0.610 and P = 0.809), or lathosterol (P = 0.388 and P = 0.102) concentrations. In addition, serum lipid and plasma glucose concentrations, and blood pressure were not changed. Conclusions Daily consumption of 4.8 g spirulina or wakame for 17 days did not affect plasma markers for intestinal cholesterol absorption or cholesterol synthesis in non-hypercholesterolemic men and women. Serum lipid and glucose concentrations, and blood pressure were also not altered.