We assessed the association of four diet quality scores with multiple cardio-metabolic outcomes among Guatemalan young adults experiencing the nutrition transition. We obtained cross-sectional dietary, demographic, anthropometric and cardio-metabolic risk factor data from 1220 Guatemalan adults (mean age 32.7 (sd 5.8) years) in 2002-4, and computed a Recommended Food Score (RFS), Not Recommended Food Score (NRFS), Food Variety Score (FVS) and the Dietary Quality Index-International (DQI-I). All four scores were correlated with energy intake (r 0.23-0.49; all P < 0.01), but had varying associations with socio-demographic characteristics, lifestyle factors and nutrient intakes. None of the scores was inversely associated with the metabolic syndrome or its components; rather some were positively associated with risk factors. Among both men and women the DQI-I was positively associated with BMI (kg/m2; beta = 0.10, 95 % CI 0.003, 0.21 (men); beta = 0.07, 95 % CI 0.01, 0.14 (women)) and waist circumference (cm; beta = 0.02, 95 % CI 0.01, 0.03 (men); beta = 0.02, 95 % CI = 0.01, 0.02 (women)). Among men, the RFS was positively associated with TAG (mg/l; beta = 0.11, 95 % CI 0.02, 0.21) and glucose (mg/l; beta = 0.13: 95 % CI 0.03, 0.22). We conclude that indices of diet quality are not consistently associated with chronic disease risk factor prevalence in this population of Guatemalan young adults.