Background: Accumulating evidence suggests that individual circulating saturated fatty acids (SFAs) are heterogeneous in their associations with cardio-metabolic diseases, but evidence about associations of SFAs with metabolic markers of different pathogenic pathways is limited. We aimed to examine associations between plasma phospholipid SFAs and metabolic markers of lipid, hepatic, glycaemic and inflammation pathways. Methods: We measured nine individual plasma phospholipid SFAs and derived three SFA groups (odd-chain: C15:0+C17:0, even-chain: C14:0+C16:0+C18:0 and very-long-chain: C20:0+C22:0+C23:0+C24:0) in individuals from the subcohort of the European Prospective Investigation into Cancer and Nutrition (EPIC)-InterAct case-cohort study across 8 European countries. Using linear regression in 15919 subcohort members, adjusted for potential confounders and corrected for multiple testing, we examined cross-sectional associations of SFAs with 13 metabolic markers. Multiplicative interactions of the 3 SFA groups with prespecified factors, including body-mass index (BMI) and alcohol consumption, were tested. Results: Higher levels of odd-chain SFA group were associated with lower levels of major lipids (total cholesterol [TC], triglycerides, apolipoprotein A-1 [ApoA1], apolipoprotein B [ApoB]) and hepatic markers (alanine transaminase [ALT], aspartate transaminase [AST], gamma-glutamyl transferase [GGT]). Higher even-chain SFA group levels were associated with higher levels of low-density-lipoprotein-cholesterol (LDL-C), TC/high-density-lipoprotein cholesterol (HDL-C) ratio, triglycerides, ApoB, ApoB/A1 ratio, ALT, AST, GGT and CRP, and lower levels of HDL-C and ApoA1. Very-long-chain SFA group levels showed inverse associations with triglycerides, ApoA1 and GGT, and positive associations with TC, LDL-C, TC/HDL-C, ApoB and ApoB/A1. Associations were generally stronger at higher levels of BMI or alcohol consumption. Conclusions: Sub-types of SFAs are associated in a differential way with metabolic markers of lipid metabolism, liver function and chronic inflammation, suggesting that odd-chain SFAs are associated with lower metabolic risk, even-chain SFAs with adverse metabolic risk, and with mixed findings for very-long-chain SFAs. Clinical and biochemical implications of these findings may vary by adiposity and alcohol intake.