Our aim was to validate a 16-item food intake questionnaire (16-FIQ) and create an easy to use method to estimate patients' nutrient intake in primary health care. Participants (52 men, 25 women) completed a 7-day food record and a 16-FIQ. Food and nutrient intakes were calculated and compared using Spearman correlation. Further, nutrient intakes were compared using kappa-statistics and exact and opposite agreement of intake tertiles. The results indicated that the 16-FIQ reliably categorized individuals according to their nutrient intakes. Methods to estimate nutrient intake based on the answers given in 16-FIQ were created. In linear regression models nutrient intake estimates from the food records were used as the dependent variables and sum variables derived from the 16-FIQ were used as the independent variables. Valid regression models were created for the energy proportion of fat, saturated fat, and sucrose and the amount of fibre (g), vitamin C (mg), iron (mg), and vitamin D (μg) intake. The 16-FIQ is a valid method for estimating nutrient intakes in group level. In addition, the 16-FIQ could be a useful tool to facilitate identification of people in need of dietary counselling and to monitor the effect of counselling in primary health care.