Despite tremendous growth in the consumption of gluten-free (GF) foods, there is a lack of evaluation of their nutritional profile and how they compare with non-GF foods. The present study evaluated the nutritional quality of GF and non-GF foods in core food groups, and a wide range of discretionary products in Australian supermarkets. Nutritional information on the Nutrition Information Panel was systematically obtained from all packaged foods at four large supermarkets in Sydney, Australia in 2013. Food products were classified as GF if a GF declaration appeared anywhere on the product packaging, or non-GF if they contained gluten, wheat, rye, triticale, barley, oats or spelt. The primary outcome was the ‘Health Star Rating’ (HSR: lowest score 0·5; optimal score 5), a nutrient profiling scheme endorsed by the Australian Government. Differences in the content of individual nutrients were explored in secondary analyses. A total of 3213 food products across ten food categories were included. On average, GF plain dry pasta scored nearly 0·5 stars less (P< 0·001) compared with non-GF products; however, there were no significant differences in the mean HSR for breads or ready-to-eat breakfast cereals (P≥ 0·42 for both). Relative to non-GF foods, GF products had consistently lower average protein content across all the three core food groups, in particular for pasta and breads (52 and 32 % less, P< 0·001 for both). A substantial proportion of foods in discretionary categories carried GF labels (e.g. 87 % of processed meats), and the average HSR of GF discretionary foods were not systematically superior to those of non-GF products. The consumption of GF products is unlikely to confer health benefits, unless there is clear evidence of gluten intolerance.