Osteoprotegerin (OPG) and B-type natriuretic peptide (BNP) are cardiovascular risk factors, interrelated with each other, with possible associations with insulin sensitivity and glucose homeostasis. The aim of this study was to assess association between OPG and BNP concentrations in a young healthy population, their relation to insulin sensitivity and obesity and their regulation by hyperinsulinemia and serum free fatty acids (FFA) elevation. The study group consisted of 59 male volunteers, 30 of whom were of a normal weight (BMI < 25 kg/m2), and 29 were overweight/obese (BMI > 25 kg/m2). Insulin sensitivity was assessed with the 2-h hyperinsulinemic-euglycemic clamp (HEC). In the subgroup of 20 subjects, the clamp was prolonged to 6 h. After one week, another 6-h clamp, with concurrent Intralipid/heparin infusion, was performed. Serum OPG was positively associated with insulin sensitivity (p = 0.002) and negatively with BMI (p = 0.019) and serum BNP (p = 0.025). In response to 6-h hyperinsulinemia, circulating BNP decreased (p < 0.001). In response to HEC with Intralipid/heparin infusion, OPG decreased (p < 0.001) and BNP increased (p < 0.001). Our data show that OPG and BNP are differentially regulated by FFA, which suggests their association with lipid-induced insulin resistance. The assessment of these cardiovascular risk factors should take into account both long-term and short-term effects associated with insulin resistance.