Socioeconomically vulnerable groups in developed countries suffer excess chronic disease due in large part to an energy dense but nutrient poor diet. Low folate can be a marker of poor dietary quality and is also affected by smoking and chronic alcohol intake, all of which cluster in groups with a low socioeconomic position. A 4.5 to 9 year follow-up study of 567 indigenous adults from remote communities in far north Queensland, Australia, from 1998 to 2007 was conducted. Analysis of the effects of demographic factors, smoking, risky alcohol drinking, fruit and vegetable intake and waist circumference on changes in red cell folate (RCF) status was conducted. Prevalence of low red cell folate doubled in the cohort from a high baseline over this seven year period: 36.9% deficient in 2007, 15.9% at baseline (p<0.001). Smoking was associated with lower folate levels. People with a normal RCF were less likely to be smokers, and were more likely to have a greater number of serves of vegetables (RR 1.06, 95% CI 1.02-1.10) than those who were deficient at follow-up. The introduction of voluntary folate fortification since 1995 does not appear to have impacted on the already poor folate status of this cohort of adults. The increased prevalence of low folate has occurred despite improvements in the food supply, indicating the need for nutrition promotion, and subsidies for healthy food in remote communities. The impact of mandatory folate fortification of flour since 2009 should be assessed in this high risk population.