Pyridoxal-5-phosphate (PLP), the active form of vitamin B6 (B6), is a co-factor for enzymes in macronutrient metabolism. Increasing protein intake may affect B6 by increasing PLP-dependent enzymes in amino acid metabolism, which may be more pronounced during moderate B6 deficiency. Decreased B6 status decreases PLP-dependent enzyme activity possibly altering macronutrient metabolism. We examined changing dietary carbohydrate: protein ratios in rats consuming recommended vs. moderately deficient intakes of pyridoxine (PN)-HCl, on plasma markers of B6 status and enzymes in intermediary metabolism. Marginal B6 deficiency decreased all plasma B6 vitamers except for pyridoxic acid. Protein intake (40% energy) significantly reduced plasma PN and tended to decrease plasma pyridoxal with no significant alterations in plasma homocysteine or cysteine. Hepatic cystathionine-γ-lyase, glycogen phosphorylase, plasma aspartate and alanine aminotransferase significantly decreased with marginal B6 deficiency and cystathionine-γ-lyase decreased with increasing protein intake. Marginal B6 deficiency significantly increased hepatic glycogen with no changes in plasma haptoglobin.